Persistent organic pollutants (POPs), such as polychlorinated biphenyls (PCBs), organochlorine pesticides (OCPs) and polybrominated diphenyl ethers (PBDEs), have a wide range of toxic effects on humans and wildlife, and have been reported in a number of endangered sea turtle populations. The present study screened for POPs in a green sea turtle Chelonia mydas population in Peninsular Malaysia and investigated the maternal transfer and effects of POPs on embryonic development. At the Ma'Daerah Turtle Sanctuary, blood, eggs and hatchling blood were collected from 11 nesting female C. mydas. Samples were analysed for 83 PCBs, 23 OCPs and 19 PBDEs using gas chromatography with tandem mass spectrometry. The chemical profiles of eggs from individual turtles were significantly different, indicating variable contaminant uptake during foraging. There was evidence of maternal transfer of POPs to eggs and hatchlings, with significant correlations in sum of PCBs (SPCB), sum of PBDEs (SPBDE), ?-hexachlorocyclohexane (?-HCH), trans-chlordane and mirex concentrations between maternal blood and eggs (p < 0.05, R2 < 0.71), between eggs and hatchling blood (p < 0.05, R2 < 0.83), and between maternal and hatchling blood (p < 0.05, R2 < 0.61). In addition, there was congener-specific transfer of PCBs with less lipophilic congeners (e.g. PCB 99) more readily transferred to hatchlings than the more lipophilic congeners (e.g. PCBs 180 + 193). There was also a significant correlation between increasing egg POP concentration and decreasing hatchling mass:length ratio. POPs may therefore have subtle effects on the development of C. mydas eggs, which may compromise offshore dispersal and predator avoidance.