From the 1940s through 1977, at least 590,000kg of polychlorinated biphenyls (PCBs) were released into the Hudson River from General Electric manufacturing plants located in Hudson Falls and Fort Edward, New York. In 1984, the U.S. Environmental Protection Agency designated a nearly 322km reach as the Hudson River PCBs Superfund Site. Here we describe a Fish Health Assessment study, part of a Natural Resource Damage Assessment, that evaluated the prevalence of toxicopathic lesions in adult brown bullhead (Ameiurus nebulosus), smallmouth bass (Micropterus dolomieu), and yellow perch (Perca flavescens). In fall 2001, 29–51 fish of each species were collected in fall 2001 from highly contaminated areas below the plants (Thompson Island Pool (TIP) and Stillwater Dam Pool (STW)), an upriver reference area (Feeder Dam Pool (FDP)), and a reference lake, Oneida Lake (ODA). The focus was on histopathologic lesions and observations associated with contaminant exposure: liver—neoplasms, foci of cellular alteration, bile duct hyperplasia; testes—ovotestis (testicular oocytes), germ cell degeneration, altered developmental stage; ovaries—atresia and altered developmental stage. Lesions associated with PCB exposure were defined as those with significantly greater prevalence and/or severity in TIP and STW compared with ODA and FDP. For brown bullhead and smallmouth bass, no lesions or changes in gonadal development met those criteria. In yellow perch, ovarian atresia was the only lesion associated with PCB exposure. Prevalence was 53% in FDP, 75% in ODA, and 100% in both STW and TIP; severity increased from mostly minimal to mild-moderate. Because of the high prevalence of atresia in reference collections, it is likely that factors other than PCBs are also involved. As part of a post–dredging monitoring plan, we recommend assessing gonad structure and function in yellow perch collected at the time of spawning in locations with a range of PCB contamination.