Van Ommen has as major research interests in the development and application of genome research and diagnostic technology for disease study, diagnosis, therapy and prevention, including the societal aspects of genetic advances. Members of his department have contributed to the finding of the gene defects and disease mechanisms underlying Duchenne Muscular Dystrophy, Huntington Disease, Polycystic Kidney Disease, FacioScapulohumeral Muscular Dystrophy, Hereditary Neuropathies, Fragile X Syndrome, Rubinstein-Taybi Syndrome, Familial Hemiplegic Migraine and Episodic Ataxia. His group has pioneered the diagnosis of genetic disease, performing the first prenatal diagnosis using DNA markers of a disease (DMD) of which the gene was (then) still unknown, developed many gene mapping techniques, generating the first megabase map of a human gene (DMD), and developed several innovative mutation detection techniques.