The institute is rooted in the Transgenic Research Center founded in 1988 and was established under the name of Ilchun Molecular Medicine Institute in 1997. ‘Ilchun’ was the pseudonym of the late Dr. and Professor Ki-Young Lee, who served as the first Chair in the Department of Medical Chemistry when Seoul National University College of Medicine was established in 1946, and founded the Korean Society for Biochemistry and Molecular Biology.

In 2007, the institute was renamed as Ilchun Genomic Medicine Institute through integration with the Human Genome Research Institute, which is called as SNU-GMI by English abbreviation. The purpose of the institute's establishment is to identify the mechanisms of disease and contribute to diagnosis, prediction, prevention, and treatment through human genomes and related bioscience studies.