Polycystic ovarian syndrome is a complex disorder with multiple factors affecting its etiology. Elucidation of specific genes and mode of inheritance remains a significant challenge. Linkage and association studies have resulted in over 50 candidate genes as a source of heritable predisposition; however, small sample sizes and failure to reproduce results have hindered efforts. In addition, low fecundity, lack of a male phenotype, and variation of diagnostic criteria represent unique challenges to discovery of polycystic ovarian syndrome genes. A concerted effort will be necessary to conclusively rule in or rule out candidate genes.