He studied medicine at the Human Medical School, Albert Ludwigs University of Freiburg, where he graduated in 1970 and received his doctoral degree in 1973.

In 1986 he received a Heisenberg scholarship of the Deutsche Forschungsgemeinschaft combined with a position as visiting professor at the Yale University, New Haven, Connecticut in the group of Laura Manuelidis and David C. Ward.

From 1996-2010 he held the position of a Full Professor, Chair of Anthropology and Human Genetics in the Faculty of Biology at the Ludwig Maximilian University of Munich.

Thomas Cremer was an early supporter of the idea that higher order chromatin arrangement and the architecture of the nucleus are essential for cardinal nuclear functions.

Together with his brother Christoph Cremer he pioneered laser-UV-microirradiation experiments that indirectly implied a territorial organization of chromosomes in the interphase nucleus.