Sustained hatchling production is a priority for leatherback sea turtle (Dermochelys coriacea) conservation. Yet the species is challenged by notoriously low hatch success, much lower than other species of sea turtles, and the result of a high rate of embryo mortality for which the causes are not understood. The aim of our study was to describe the pathology of embryos and dead-in-nest hatchlings, to help understand the basis for low hatch success in St. Kitts, West Indies. We surveyed two leatherback nesting beaches, Keys and North Friars, in 2015–16. Pathology was present in 38% (32 of 84) of individuals, including renal mineralization (24%, 20 of 83), bacterial pneumonia (12%, 10 of 82), and skeletal muscle necrosis (7%, 6 of 84). Renal mineralization was seen in all stages of development that we examined and was associated with cardiac mineralization in two cases. Bacterial pneumonia affected dead-in-nest hatchlings and late-stage embryos and involved 40% (6 of 15) of nests evaluated, all laid by different mothers. Hematopoiesis was consistently observed in the liver, lung, kidneys, and heart. Gonad was histologically classified as female in 100% (68 of 68) of individuals examined. Rathke's gland was identified in the axillary musculature of 51 individuals, which has not previously been described in leatherbacks. Bacterial pneumonia and renal mineralization were presumed to be significant causes of death in leatherback embryos and hatchlings in St. Kitts. Overrepresentation of females in our study suggested high incubation temperatures in the nests.