As top predators, crocodilians can bioaccumulate high concentrations of persistent organochlorine pesticides (OCPs) that may have adverse effects on their physiology and health. Recent and illegal uses of OCPs in Mexico could affect populations of the American crocodile (Crocodylus acutus), already threatened by other factors. We analyzed 16 OCP compounds using gas chromatography with electron capture detection in seven infertile eggs and in the substratum of nine nests of American crocodiles in Banco Chinchorro, an atoll off the Mexican coast of the Yucatan peninsula. Nest type, clutch size and distance from nests to nearest lagoon were also recorded, while total length of the females attending each nest was measured directly or estimated. Although Banco Chinchorro is isolated from the mainland and from known sources of contamination, OCP residues were detected in egg and nest substratum samples collected from the atoll. OCP concentrations in eggs (range: 0.002–4.000 ppb) and nest substrata (range: 0.01–1.82 ppb) are ten to thousands times lower compared to other studies. Total OCP concentration (sum of all OCPs) in nest substrata decreased with increasing distance from the shore, suggesting that eggs deposited farther from the shore were less exposed to OCP absorption from substratum. Total OCP concentrations in eggs were positively correlated with total length of females and thus with their age. We speculate that maternal transfer from laying females is likely the major source of contaminants in eggs. Future investigations are needed to identify the origin of contaminants in Banco Chinchorro.