Investigating environmental pollution is important to understand its impact on endangered species such as green turtles (Chelonia mydas). In this study, we investigated the accumulation and potential toxicity of selected persistent organic pollutants (POPs) and naturally occurring MeO-PBDEs in liver, fat, kidney and muscle of turtles (n = 30) of different gender, size, year of death, location and health status. Overall, POP concentrations were low and accumulation was highest in liver and lowest in fat which is likely due to the poor health of several animals, causing a remobilization of lipids and associated compounds. PCBs and p,p'-DDE dominated the POP profiles, and relatively high MeO-PBDE concentrations (2'-MeO-BDE 68 up to 192 ng/g lw, 6-MeO-BDE 47 up to 79 ng/g lw) were detected in all tissues. Only few influences of factors such as age, gender and location were found. While concentrations were low compared to other marine wildlife, biological toxicity equivalences obtained by screening the tissue extracts using the micro-EROD assay ranged from 2.8 to 356 pg/g and the highest values were observed in muscle, followed by kidney and liver. This emphazises that pollutant mixtures found in the turtles have the potential to cause dioxin-like effects in these animals and that dioxin-like compounds should not be overlooked in future studies.