The African sharptooth catfish (Clarias gariepinus) is indigenous to South Africa where it is commonly found in calm waters such as lakes, streams, rivers, swamps and floodplains. The males of this gonochoristic species can be readily distinguished from females via a distinct elongated urogenital papilla with a pointed tip, located just behind the anus. This structure is an androgen controlled secondary sexual characteristic and could potentially be affected by chemicals displaying endocrine disrupting properties during development. Results of previous studies on effects on papillae of different fish species indicated that these structures could be useful as bio-indicators of exposure due to alterations in the structures. This study investigated the occurrence of abnormal morphology in urogenital papillae compared to the macroscopic and microscopic structure of the gonads of presumed male or intersex catfish sampled from the Rietvlei and Marais dams in an urban nature reserve, due to exposure to endocrine disrupting chemicals (EDCs). Macroscopic observation of the UGP, gonad examination after laparotomy and histology were done. Gonadosomatic index (GSI) and Urogenital papilla length index (UGPLI) were determined for all fish collected. Mesenteric fat analyzed for selected alkylphenols and organochlorines showed high levels of especially nonylphenol indicating long term exposure to these chemicals due to bio-accumulation. The GSI indicated that fish with intersex gonads were probably feminized males. It was concluded that use of the UGP alone, without macroscopic and microscopic analyses of the gonads, could not effectively indicate exposure to EDCs.