Since the early 1900s, the lakes of the Ocklawaha basin in central Florida have experienced ecological degradation due to anthropogenic development. One species affected by this degradation is the American alligator Alligator mississippiensis, which has suffered from poor clutch viability and embryo mortality. Although some studies indicate that organochlorine pesticides (OCPs) may be involved, OCPs do not account for all of the variation seen in hatch rates. Indeed, nutrition and non-OCP contaminants have been associated with developmental problems in fish and birds. Our study evaluated embryo mortality in alligators at reference and OCP-contaminated sites as a function of exposure to OCPs, polychlorinated biphenyls (PCBs), and polyaromatic hydrocarbons (PAHs), along with egg nutrients (Zn, Se, and vitamins A, E, and B1). The four-pronged study consisted of a case-control cohort study, an expanded field study, a topical egg treatment thiamine amelioration experiment, and a topical egg treatment thiamine antagonist experiment. The results from the two field studies suggested that the total thiamine levels in the eggs were positively associated with clutch viability and negatively associated with the lipid content and certain OCPs measured in egg yolks. In addition, PCBs, PAHs, Zn, Se, and vitamins A and E were not found to be associated with the observed clutch viability defects. The thiamine levels in the eggs explained 38% of the variation in clutch survival in the case-control cohort study and 27% in the expanded field study. The topical egg treatment experiments were successful in elevating the thiamine concentrations in the albumin but not the yolk. No significant differences were noted among treatment groups in either egg treatment experiment with respect to clutch survival. In summary, thiamine egg concentrations explain some of the variation in the clutch viability of free-ranging alligators, but the cause-effect relationships are still unclear.