Organochlorine compounds (OCs), including polychlorinated biphenyls and organochlorine pesticides, were used on lands adjacent to the Middle Mississippi River (MMR; USA) from 1930 through 1988, and they continue to occur in MMR fish. These compounds are estrogenic and/or antiandrogenic, and they alter hormone production and reception within the brain and gonads of male fish, resulting in intersexuality and/or suppressed gonadal development. To assess how OCs affect reproduction of MMR fish, we quantified OC accumulation, intersexuality, and gonadal development in male shovelnose sturgeon (Scaphirhynchus platorynchus) throughout the MMR during the spring of 2003. Gonads were observed for intersexual characteristics, weighed to calculate the gonadosomatic index (GSI), and examined histologically. Tissue accumulation of OCs was quantified in gonads, brain-hypothalamic-pituitary (BHP) complex, and fillets. Four of 48 mature males were identified macroscopically as intersexuals, and a fifth was found through histology (a 10.4% incidence). Intersexuals accumulated higher concentrations of OCs in the BHP complex compared with those of mature males. In addition, GSI and OC accumulation within the BHP complex, gonads, and fillets of mature males were negatively related. Exposure to OCs before or during sexual differentiation likely induces intersexuality in MMR shovelnose sturgeon, and exposure throughout gonadal maturation inhibits gonadal development.