Boveri's work with sea urchins showed that it was necessary to have all chromosomes present in order for proper embryonic development to take place. This discovery was an important part of the Boveri - Sutton chromosome theory. His other significant discovery was the centrosome (1888), which he described as the especial organ of cell division. Boveri also discovered the phenomenon of chromatin diminution during embryonic development of the nematode Parascaris.

He also reasoned in 1902 that a cancerous tumor begins with a single cell in which the makeup of its chromosomes becomes scrambled, causing the cells to divide uncontrollably. He proposed the existence of cell - cycle checkpoints, tumour suppressor genes, and oncogenes and that aberrant mitoses and uncontrolled growth might be caused by radiation, physical or chemical insults or by microscopic pathogens. It was only later that researchers such as Thomas Hunt Morgan in 1915 demonstrated that Boveri was correct.