Henry's first tutor was Bruno, Bishop of Augsburg. On Bruno's death in 1029, Egilbert, Bishop of Freising, was appointed to take his place. In 1033, at the age of sixteen, Henry came of age and Egilbert was compensated for his services. In 1035, Adalbero, Duke of Carinthia, was deposed by Conrad, but Egilbert convinced Henry to refuse this injustice and the princes of Germany, having legally elected Henry, would not recognise the deposition unless their king did also. Henry, in accordance with his promise to Egilbert, did not consent to his father's act and Conrad, stupefied, fell unconscious after many attempts to turn Henry. Upon recovering, Conrad knelt before his son and exacted the desired consent. Egilbert was penalised dearly by the emperor.

In 1036, Henry was married to Gunhilda of Denmark. She was a daughter of Canute the Great, King of Denmark, England, and Norway, by his wife Emma of Normandy. Early on, Henry's father had arranged with Canute to have him rule over some parts of northern Germany (Kiel) and in turn to have their children married. The marriage took place in Nijmegen at the earliest legal age.

In 1038, Henry was called to aid his father in Italy (1038) and Gunhilda died on the Adriatic Coast, during the return trip (during the same epidemic in which Herman IV of Swabia died). In 1039, his father, too, died and Henry became sole ruler and imperator in spe.
Henry spent his first year on a tour of his domains. He visited the Low Countries to receive the homage of Gothelo I, Duke of Upper and Lower Lorraine. In Cologne, he was joined by Herman II, Archbishop of Cologne, who accompanied him and his mother to Saxony, where he was to build the town of Goslar up from obscurity to stately imperial grandeur. He had an armed force when he entered Thuringia to meet with Eckard II, Margrave of Meissen, whose advice and counsel he desired on the recent successes of Duke Bretislaus I of Bohemia in Poland. Only a Bohemian embassy bearing hostages appeased Henry and he disbanded his army and continued his tour. He passed through Bavaria where, upon his departure, King Peter Urseolo of Hungary sent raiding parties into Swabia. There, at Ulm, he convened a Fürstentag at which he received his first recognition from Italy. He returned to Ingelheim after that and there was recognised by a Burgundian embassy and Aribert, Archbishop of Milan, whom he had supported against his father. This peace with Aribert healed the only open wound in the Empire. Meanwhile, in 1039, while he was touring his dominions, Conrad, Adalbero's successor in Carinthia and Henry's cousin, died childless. Henry being his nearest kin automatically inherited that duchy as well. He was now a triple - duke (Bavaria, Swabia, Carinthia) and triple - king (Germany, Burgundy, Italy).

Henry's first military campaign as sole ruler took place then (1040). He turned to Bohemia, where Bretislaus was still a threat, especially through his Hungarian ally's raiding. At Stablo, after attending to the reform of some monasteries, Henry summoned his army. In July, he met with Eckhard at Goslar and joined together his whole force at Regensburg. On 13 August, he set out. He was ambushed and the expedition ended in disaster. Only by releasing many Bohemian hostages, including Bretislaus's son, did the Germans procure the release of many of their comrades and the establishment of a peace. Henry retreated hastily and with little fanfare, preferring to ignore his first great defeat. On his return to Germany, Henry appointed Suidger bishop of Bamberg. He would later be Pope Clement II.

In 1040, Peter of Hungary was overthrown by Samuel Aba and fled to Germany, where Henry received him well despite the enmity formerly between them. Bretislaus was thus deprived of an ally and Henry renewed preparations for a campaign in Bohemia. On 15 August, he and Eckard set out once more, almost exactly a year after his last expedition. This time he was victorious and Bretislaus signed a peace treaty at Regensburg.

He spent Christmas 1041 at Strasbourg, where he received emissaries from Burgundy. He travelled to that kingdom in the new year and dispensed justice as needed. On his return, he heard, at Basel, of the raids into Bavaria being made by the king of Hungary. He thus granted his own duchy of Bavaria to one Henry, a relative of the last independent duke. At Cologne, he called together all his great princes, including Eckard, and they unanimously declared war on Hungary. It wasn't until September 1042 that he set out, after having dispatched men to seek out Agnes de Poitou to be his new bride. The expedition into Hungary successfully subdued the west of that nation, but Aba fled to eastern fortresses and Henry's installed candidate, an unknown cousin of his, was quickly removed when the emperor turned his back.

After Christmas at Goslar, his intended capital, he entertained several embassies: Bretislaus came in person, a Kievan embassy was rejected because Henry was not seeking a Rus bride, and the ambassadors of Casimir I of Poland were likewise rejected because the duke came not in person. Gisela, Henry's mother, died at this juncture and Henry went to the French borders, probably near Ivois to meet King Henry I of France, probably over the impending marriage to the princess of Aquitaine. Henry next turned to Hungary again, where he forced Aba to recognise the Danubian territory donated to Germany by Stephen I of Hungary pro causa amicitiae (for friendship's sake). These territories were ceded to Hungary after the defeat of Conrad II in 1030. This border remained the border between Hungary and Austria until 1920.

After this victory, Henry, a pious man, who dreamed of a Peace and Truce of God being respected over all his realms, declared from the pulpit in Konstanz in October 1043 a general indulgence or pardon whereby he promised to forgive all injuries to himself and to forgo vengeance. He encouraged all his vassals to do likewise. This is known as the "Day of Indulgence" or "Day of Pardon".

Henry was finally remarried at Ingelheim in 1043 to Agnes, daughter of duke William V of Aquitaine and Agnes of Burgundy. Agnes was then living at the court of her stepfather, Geoffrey Martel, count of Anjou. This connection to the obstreperous vassal of the French king as well as her consanguinity — she and Henry being both descended from Henry the Fowler — caused some churchmen to oppose their union, but the marriage went as planned. Agnes was crowned at Mainz.

After the coronation and the wedding, Henry wintered at Utrecht, where he proclaimed the same indulgence he had proclaimed the year prior in Burgundy. Then, in April 1044, Gothelo I, Duke of Lorraine, that is of both Lower and Upper Lorraine, died. Henry did not wish to solidify the ducal power in any duchy and so, instead of appointing Godfrey, Gothelo's eldest son and already acting duke in Upper Lorraine, duke in the Lower duchy, he appointed Gothelo II, Godfrey's younger brother, duke there, thus raising the eldest son's ire. Henry claimed that Gothelo's dying wish was to see the duchy split between the brothers, but Godfrey, having faithfully served Henry thus far, rebelled. Henry called the two brothers together at Nijmegen, but failed to reconcile them. Nevertheless, he set out on the war path against Hungary, then experiencing internal duress.

Henry entered Hungary on 6 July and met a large army with his small host. Disaffection rent the Magyar forces, however, and they crumbled at the German onslaught in the Battle of Ménfő. Peter was reinstalled as king at Székesfehérvár, a vassal of the Empire, and Henry could return home triumphant, the Hungarian people having readily submitted to his rule. Tribute was to be paid and Aba, while fleeing, was captured by Peter and beheaded. Hungary appeared to have entered the German fold fully and with ease.

Upon his return from the Hungarian expedition, Godfrey of Lorraine began seeking out allies, among them Henry of France, to support him in any possible act of overt insurrection. Seeing this, the emperor summoned Henry to a trial by his peers of Lower Lorraine at Aachen where he was condemned and his duchy and county of Verdun (a royal fief) seized. He immediately fled the scene and began arming for revolt. Henry wintered at Speyer, with the civil war clearly in view on the horizon.

In early 1045, Henry entered Lorraine with a local army and besieged Godfrey's castle of Bockelheim (near Kreuznach) and took it. He took a few other castles, but famine drove him out. Leaving behind enough men to guard the countryside against Godfrey's raids, he turned to Burgundy. Godfrey had done his best to foment rebellion in that kingdom by playing of the imperialist, which supported union with the empire, and nationalist, which supported an independent Burgundy, factions against each other. However, Louis, Count of Montbéliard, defeated Reginald I, Count of Burgundy (what was to become the Free County), and when Henry arrived, the latter was ready with Gerald, Count of Geneva, to do homage. Burgundy was thereafter happily united to Henry's crown.

Then, Henry discussed the Italian political scene with some Lombard magnates at Augsburg and then went on to Goslar, where he gave the duchy of Swabia to Otto, Count Palatine of Lorraine. Henry also gave the march of Antwerp to Baldwin, the son of Baldwin V of Flanders. On his way to Hungary, to spend Pentecost with King Peter, a floor collapsed in one of his halls and Bruno, Bishop of Würzburg, was killed. In Hungary, Peter gave over the golden lance, symbol of sovereignty in Hungary, to Henry and pledged an oath of fealty along with his nobles. Hungary was now pledged to Peter for life and peace was fully restored between the two kingdoms of Germany and Hungary. In July, even Godfrey submitted and was imprisoned in Gibichenstein, the German Tower.

Henry fell ill at Tribur in October and Henry of Bavaria and Otto of Swabia chose as his successor Otto's nephew and successor in the palatinate, Henry I. Henry III, however, recovered, still heirless. At the beginning of the next year, now at the height of his power, but having divested himself of two of the great stem duchies, Henry's old advisor, Eckard of Meissen, died, leaving Meissen to Henry. Henry bestowed it on William, count of Orlamünde. He then moved to Lower Lorraine, where Gothelo II had just died and Dirk IV of Holland had seized Flushing. Henry personally led a river campaign against Count Dirk. Both count and Flushing fell to him. He gave the latter to Bernold, Bishop of Utrecht, and returned to Aachen to celebrate Pentecost and decide on the fate of Lorraine. Henry pitied and restored Godfrey, but gave the county of Verdun to the bishop of the city. This did not conciliate the duke. Henry gave the lower duchy to Frederick. He then appointed Adalbert archbishop of Bremen and summoned Widger, Archbishop of Ravenna, to a trial. The right of a German court to try an Italian bishop was very controversial and presaged the Investiture Controversy that characterised the reigns of Henry's son and grandson. Henry continued from there on to Saxony and held imperial courts at Quedlinburg, Merseburg (June), and Meissen. At the first, he made his daughter Beatrice from his first marriage abbess and at the second, he ended the strife between the dux Bomeraniorum and Casimir of Poland. This is one of the earliest, or perhaps the earliest, recording of the name of Pomerania, whose duke, Zemuzil, brought gifts.

It was after the these events in northern Germany and a brief visit to Augsburg, where he summoned the greatest magnates, clerical and lay, of the realm to meet him and accompany him, that he crossed the Brenner Pass into Italy, one of the most important of his many travels. His old ally, Aribert of Milan, had recently died and the Milanese had chosen as candidate for his successor one Guido, in opposition to the nobles' candidate. Meanwhile, in Rome, three popes — Benedict IX, Sylvester III, and Gregory VI — contested the pontifical honours. Benedict was a Tusculan who had previously renounced the throne, Sylvester was a Crescentian, and Gregory was a reformer, but a simoniac. Henry marched first to Verona, thence to Pavia in October. He held a court and dispensed justice as he had in Burgundy years earlier. He moved on to Sutri and held a second court on 20 December whereat he deposed all the candidates for the Saint Peter's throne and left it temporarily vacant. He headed towards Rome and held a synod wherein he declared no Roman priest fit. Adalbert of Bremen refused the honour and Henry appointed Suidger of Bamberg, who was acclaimed duly by the people and clergy, we are told. He took the name Clement II.

On 25 December, Christmas Day, Clement was consecrated and Henry and Agnes were crowned Holy Roman Emperor and Empress. The populace gave him the golden chain of the patriciate and made him patricius, giving the powers, seemingly, of the Crescentii family during the tenth century: the power to nominate popes. Henry's first acts were to visit Frascati, capital of the counts of Tusculum, and seize all the castles of the Crescentii. He and the pope then moved south, where his father had created the situation as it was then in his visit of 1038. Henry reversed many of Conrad's acts. At Capua, he was received by Prince Guaimar IV of Salerno, also Prince of Capua since 1038. However, Henry gave Capua back to the twice - deprived Prince Pandulf IV, a highly unpopular choice. Guaimar had been acclaimed as Duke of Apulia and Calabria by the Norman mercenaries under William Iron Arm and his brother Drogo of Hauteville. In return, Guaimar had recognised the conquests of the Normans and invested William as his vassal with the comital title. Henry made Drogo, William's successor in Apulia, a direct vassal of the imperial crown. He did likewise to Ranulf Drengot, the count of Aversa, who had been a vassal of Guaimar as Prince of Capua. Thus, Guaimar was deprived of his greatest vassals, his principality split in two, and his greatest enemy reinstated. Henry lost popularity amongst the Lombards with these decisions and Benevento, though a papal vassal, would not admit him. He authorised Drogo to conquer it and headed north to reunion with Agnes at Ravenna. He arrived at Verona in May and the Italian circuit was completed.

On Henry's return to Germany, many offices which had fallen vacant were filled. First, Henry gave away his last personal duchy: he made Welf duke of Carinthia. He made his Italian chancellor, Humphrey, archbishop of Ravenna. He filled several other sees: he installed Guido in Piacenza, his chaplain Theodoric in Verdun, the provost Herman of Speyer in Strasbourg, and his German chancellor Theodoric in Constance. The important Lorrainer bishoprics of Metz and Trier received respectively Adalberon and Eberhard, a chaplain.

The many vacancies of the Imperial episcopate now filled, Henry was at Metz (July 1047) when the rebellion then stewing broke out seriously. Godfrey was now allied with Baldwin of Flanders, his son (the margrave of Antwerp), Dirk of Holland, and Herman, Count of Mons. Henry gathered an army and went north, where he gave Adalbert of Bremen lands once Godfrey's and oversaw the trial by combat of Thietmar, the brother of Bernard II, Duke of Saxony, accused of plotting to kill the king. Bernard, an enemy of Adalbert's, was now clearly on Henry's bad side. Henry made peace with the new king of Hungary, Andrew I and moved his campaign into the Netherlands. At Flushing, he was defeated by Dirk. The Hollanders sacked Charlemagne's palace at Nijmegen and burnt Verdun. Godfrey then made public penance and assisted in rebuilding Verdun. The rebels besieged Liège, defended stoutly by Bishop Wazo. Henry slowed his campaigning after the death of Henry of Bavaria and gave Upper Lorraine to one Adalbert and left. The pope had died in the meantime and Henry chose Poppo of Brixen, who took the name Damasus II. Henry gave Bavaria to one Cuno and, at Ulm in January 1048, Swabia to Otto of Schweinfurt, called the White. Henry met Henry of France, probably at Ivois again, in October and at Christmas, envoys from Rome came to seek a new pope, Damasus having died. Henry's most enduring papal selection was Bruno of Toul, who took office as Leo IX, and under whom the Church would be divided between East and West. Henry's final appointment of this long spate was a successor to Adalber in Lorraine. For this, he appointed Gerard of Chatenoy, a relative of Adalbert and Henry himself.

The year of 1049 was a series of successes. Dirk of Holland was defeated and killed. Adalbert of Bremen managed a peace with Bernard of Saxony and negotiated a treaty with the missionary monarch Sweyn II of Denmark. With the assistance of Sweyn and Edward the Confessor of England, whose enemies Baldwin had harboured, Baldwin of Flanders was harassed by sea and unable to escape the onslaught of the imperial army. At Cologne, the pope excommunicated Godfrey, in revolt again, and Baldwin. The former abandoned his allies and was imprisoned by the emperor yet again. Baldwin too gave in under the pressure of Henry's ravages. Finally, war had ceased in the Low Countries and the Lorraines and peace seemed to have taken hold.

In 1051, Henry undertook a third Hungarian campaign, but failed to achieve anything lasting. Lower Lorraine gave trouble again, Lambert, Count of Louvain, and Richildis, widow Herman of Mons, and new bride of Baldwin of Antwerp, were causing strife. Godfrey was released and to him was it given to safeguard the unstable peace attained two years before.

In 1052, a fourth campaign was undertaken against Hungary and Pressburg (modern Bratislava) was besieged. Andrew of Hungary called in the pope's mediation, but upon Henry's lifting of the siege, Andrew withdrew all offers of tribute and Leo IX excommunicated him at Regensburg. Henry was unable immediately to continue his campaign, however. In fact, he never renewed it in all his life. Henry did send a Swabian army to assist Leo in Italy, but he recalled it quickly. In Christmas of that year, Cuno of Bavaria was summoned to Merseburg and deposed by a small council of princes for his conflicting with Gebhard III, Bishop of Regensburg. Cuno revolted.

In 1053, at Tribur, the young Henry, born 11 November 1050, was elected king of Germany. Andrew of Hungary almost made peace, but Cuno convinced him otherwise. Henry appointed his young son duke of Bavaria and went thence to deal with the ongoing insurrection. Henry sent another army to assist Leo in the Mezzogiorno against the Normans he himself had confirmed in their conquests as his vassal. Leo, sans assistance from Guaimar (distanced from Henry since 1047), was defeated at the Battle of Civitate on 18 June 1053 by Humphrey, Count of Apulia; Robert Guiscard, his younger brother; and Prince Richard I of Capua. The Swabians were cut to pieces.

In 1054, Henry went north to deal with Casimir of Poland, now on the warpath. He transferred Silesia from Bretislaus to Casimir. Bretislaus nevertheless remained loyal to the end. Henry turned westwards and crowned his young son at Aachen on July 17 and then marched into Flanders, for the two Baldwins were in arms again. John of Arras, who had seized Cambrai before, had been forced out by Baldwin of Flanders and so turned to the Emperor. In return for inducing Liutpert, Bishop of Cambrai, to give John the castle, John would lead Henry through Flanders. The Flemish campaign was a success, but Liutpert could not be convinced.

Bretislaus, who had regained Silesia in a short war, died that year. The margrave Adalbert of Austria, however, successfully resisted the depredations of Cuno and the raids of the king of Hungary. Henry could thus direct his attention elsewhere than rebellions for once. He returned to Goslar, the city where his son had been born and which he had raised to imperial and ecclesiastic grandeur with his palace and church reforms. He passed Christmas there and appointed Gebhard of Eichstedt as the next holder of the Petrine see, with the name Victor II. He was the last of Henry's four German popes.

In 1055, Henry soon turned south, to Italy again, for Boniface III of Tuscany, ever an imperial ally, had died and his widow, Beatrice of Barhad married Godfrey of Lorraine (1054). Firstly, however, he gave his old hostage, Spitignev, the son of Bretislaus to the Bohemians as duke. Spitignev did homage and Bohemia remained securely, loyally, and happily within the Imperial fold. By Easter, Henry had arrived in Mantua. He held several courts, one at Roncaglia, where, a century later (1158), Frederick Barbarossa held a far more important diet, sent out his missi dominici to establish order. Godfrey, ostensibly the reason for the visit, was not well received by the people and returned to Flanders. Henry met the pope at Florence and arrested Beatrice, for marrying a traitor, and her daughter Matilda, later to be such an enemy of Henry's son. The young Frederick of Tuscany, Beatrice' son, refused to come to Florence and died within days. Henry returned via Zürich and there betrothed his young son to Bertha, daughter of Count Otto of Savoy.

Henry entered a Germany in turmoil. A staunch ally against Cuno in Bavaria, Gebhard of Regensburg, was implicated in a plot against the king along with Cuno and Welf of Carinthia. Sources diverge here: some claim only that these princes' retainers plotted the king's undoing. Whatever the case, it all came to naught and Cuno died of plague, Welf soon following him to the grave. Baldwin of Flanders and Godfrey were at it again, besieging Antwerp. They were defeated, again. Henry's reign was clearly changing in character: old foes were dead or dying and old friends as well. Herman of Cologne died. Henry appointed his confessor, Anno, as Herman's successor. Henry of France, so long eyeing Lorraine greedily, met for a third time with the emperor at Ivois in May 1056. The French king, not renowned for his tactical or strategic prowess, but admirable for his personal valour on the field, had a heated debate with the German king and challenged him to single combat. Henry fled at night from this meeting. Once in Germany again, Godfrey made his final peace and Henry went to the northeast to deal with a Slav uprising after the death of William of Meissen. He fell ill on the way and took to bed. He freed Beatrice and Matilda and had those with him swear allegiance to the young Henry, whom he commended the pope, present. On 5 October, not yet forty, Henry died. His heart went to Goslar, his body to Speyer, to lie next to his father's in the family vault in the cathedral of Speyer. He had been one of the most powerful of the Holy Roman Emperors: his authority as king in Burgundy, Germany, and Italy only rarely questioned, his power over the church was at the root of what the reformers he sponsored later fought against in his son, and his achievement in binding to the empire her tributaries was clear. Nevertheless, his reign is often pronounced a failure in that he apparently left problems far beyond the capacities of his successors to handle. The Investiture Controversy was largely the result of his church politics, though his popemaking gave the Roman diocese to the reform party. He united all the great duchies save Saxony to himself at one point or another, but gave them all away. His most enduring and concrete monument may be the impressive palace (kaiserpfalz) at Goslar.