Theodor Boveri was born in Bamberg, Germany, the son of a doctor. Boveri was artistically inclined. He initially enrolled to study the humanities, but in 1881, Boveri entered the University of Munich to study anatomy and biology. He graduated with his doctorate - summa cum laude - in 1885, with the thesis, Beiträge zur Kenntnis der Nervenfasern (On the Study of Nerve Fibers). He received a scholarship, and was able to continue doing independent research at the zoology department in Munich.

In the late 1880's and early 1890's, Boveri published some of his most significant findings. Oskar Hertwig had already discovered that sperm and egg nuclei fuse during fertilization. Boveri studied the maturation of egg cells of Ascaris megalocephala, the horse nematode. He saw that as egg cells matured, there comes a point where chromosome numbers are reduced in half. Boveri was one of the first to see evidence of the process of meiosis.

Boveri was also one of the first to do experiments in the field of cytology. He chronicled the development of sea urchin eggs, when one egg was fertilized by two sperm. He concluded that male sperm nuclei and female egg nuclei were equivalent in the amount of hereditary information. They each had a half set (haploid number) of chromosomes. As long as there was a set of both (diploid number of chromosomes), there was fairly normal development of the sea urchin larvae. Any more or any less and there was abnormal development. When Mendel's laws were rediscovered in 1900, Boveri recognized the correlation between Mendel's factors and the cytology work being done on chromosomes.

In 1893, Boveri was appointed Professor of Zoology and Comparative Anatomy at the University of Würzburg. In 1902 and 1908, Nettie Stevens spent time in Boveri's lab, and likely was influenced by his cytology work. Boveri was not overly fond of Stevens, and complained about how she was a "bloodsucker," learning much but contributing little.

Boveri remained at the University of Würzburg until his death in 1915.