The BiGCaT Bioinformatics group, the predecessor of the Department of Bioinformatics- BiGCaT, was born in 2001. It was a collaboration the faculty of Biomedical Engineering at the Technische Universiteit Eindhoven , the Cardiovascular Research Institute Maastricht (CARIM) and the Nutrition and Toxicology Research Institute Maastricht (NUTRIM).

The department is now embedded in the Faculty of Health Medicine and Life Sciences (FHML) and is one of the constituent departments of the NUTRIM School for Nutrition, Toxicology and Metabolism.