Many factors threaten the survival of marine turtles, such as incidental capture by fisheries, habitat degradation, pollution and diseases. One of the most important diseases is fibropapillomatosis (FP), characterized by the development of benign skin tumours. FP predominantly affects juvenile green sea turtles (Chelonia mydas) and involves a complex multifactorial aetiology. For several years, it has been noted that the prevalence of FP tends to be higher in marine environments under the influence of human activities, leading to the hypothesis that environmental pollutants play a role in the epidemiology of this disease. Organochlorine compounds (OCs) are persistent organic pollutants with immunosuppressive and carcinogenic effects in humans and wildlife. OC levels (α-BHC, β-BHC, α-endosulphan, β-endosulphan, endosulphan sulphate, pp′-DDD, op′-DDD, pp′-DDE, op′-DDE, heptachlor, dicofol and mirex) were quantified through gas chromatography with a micro-electron capture detector (GC-μECD) in liver and fat samples from 64 juvenile green sea turtles. Specimens with and without FP were analysed, after being caught at three feeding areas off the Brazilian coast: Ubatuba, Praia Grande and Vitória. OC levels were comparable to those observed in similar studies, and no consistent difference was observed between sea turtles with and without FP. This study helps to elucidate the contamination profile in sea turtles caught at feeding areas off Brazil and confirms that green sea turtles are exposed to OCs, which may play a negative role in the health of this species.