The Department of Biology was established in 1919, shortly after Masaryk University and its Faculty of Medicine were founded. At the beginning it was housed in the old military barracks on Údolni Street no. 73.

The first to chair it were Edward Babák, physiologist, and František K. Studnička, histologist, who both focused primarily on teaching general biology.

Experimental studies started when Jan Bělehrádek joined the Department in 1924. His studies of the effects of temperature on living processes made him know world-wide particularly after his monograph Temperature and Living Matter was published in 1935. In his pedagogical career he achieved great respect with the outstanding textbook General Biology. This had five editions, of which the last appeared in 1946.

Between 1935 and 1937 first Vilém Laufberger and then Ludvík Drastich, both physiologists, held the chair in the department.

A new era for the department came in 1937 with Ferdinand Herčík, then a renowned biophysicist. After the war the department moved into the building on Joštova Street, no.10, where all science departments were located. Soon, F. Herčík gathered a team of enthusiastic and dedicated co-workers who were interested not only in radiobiology, but also in virology and cytology. Together with his students he first set up a biophysical laboratory and, in 1955, he founded the Institute of Biophysics at the Czechoslovak Academy of Sciences. F. Herčík himself was interested in general biophysics (quantum biology), bacteriophage morphogenesis and electron microscopy.

In 1960, Oldřich Nečas, a former Herčík's student, was appointed Head of the department. He focused on yeast cells and protoplasts and on protozoans as model systems for extensive studies of cell morphogenesis. Jan Šmarda, another of Herčík's students, and his group were involved in studies on the biology of bacteriocins.

In 1992 the former Nečas' student Augustin Svoboda was named Head of the department. In the early 1990s supported by grants and promoted by international contacts, research in biology began to diversify, giving rise to new projects, namely molecular biology of bacteriocins, Treponema genome analysis, and investigation into cell cytoskeletons, cell stress and apoptosis.

In 2005 the Department of Biology moved to new buildings of the University Campus in Brno-Bohunice and Petr Dvořák was appointed to head the Department. Under his leadership research at the Department of Biology is being incorporated into broad international cooperation in the field of stem cell biology and its medical application.