Threatened or endangered reptiles, such as sea turtles, are generally understudied within the field of wildlife toxicology, with even fewer studies on how contaminants affect threatened species reproduction. This paper aimed to better inform threatened species conservation by systematically and quantitatively reviewing available research on the reproductive toxicology of all reptiles, threatened and non-threatened. This review found 178 studies that matched our search criteria. These papers were categorized into location conducted, taxa studied, species studied, effects found, and chemicals investigated. The most studied taxa were turtles (n = 87 studies, 49%), alligators/crocodiles (n = 54, 30%), and lizards (n = 37, 21%). Maternal transfer, sex steroid alterations, sex reversal, altered sexual development, developmental abnormalities, and egg contamination were the most common effects found across all reptile taxa, providing guidance for avenues of research into threatened species. Maternal transfer of contaminants was found across all taxa, and taking into account the foraging behavior of sea turtles, could help elucidate differences in maternal transfer seen at nesting beaches. Sex steroid alterations were a common effect found with contaminant exposure, indicating the potential to use sex steroids as biomarkers along with traditional biomarkers such as vitellogenin. Sex reversal through chemical exposure was commonly found among species that exhibit temperature dependent sex determination, indicating the potential for both environmental pollution and climate change to disrupt population dynamics of many reptile species, including sea turtles. Few studies used in vitro, DNA, or molecular methodologies, indicating the need for more research using high-throughput, non-invasive, and cost-effective tools for threatened species research. The prevalence of developmental abnormalities and altered sexual development and function indicates the need to further study how anthropogenic pollutants affect reproductive output in threatened reptiles.