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Bioaccumulation of environmental contaminants has been documented in amphibians and reptiles inhabiting the Great Lakes, St. Lawrence River and elsewhere. The effects of pollutants on the physiology and reproduction of amphibians and reptiles has also been reported but this research has largely been restricted to laboratory studies. Much less work has been conducted to quantify the effects of toxic chemical exposures on these cryptic animals in the wild. In the Great Lakes basin and St. Lawrence River, this work has only been performed in detail since 1981 although some samples collected in 1974 indicated a high level of contamination. Results in the 1990s on aquatic salamanders, frogs and turtles indicate that adults and embryos are currently experiencing toxic effects and, in some species and locations, there are indications that population declines are influenced by environmental pollution exposure. In this review, we describe the existing literature on contaminant levels and effects in reptiles and amphibians of the St. Lawrence River and Great Lakes basin.