ABSTRACT: The completion of embryonic development depends, in part, on the interplay between genetic factors and environmental conditions, and any alteration during development may affect embryonic genetic and epigenetic regulatory pathways leading to congenital malformations, which are mostly incompatible with life. Oviparous reptiles, such as sea turtles, that produce numerous eggs in a clutch that is buried on the beach provide an opportunity to study embryonic mortality associated with malformations that occur at different times during development, or that prevent the hatchling from emerging from the nest. In sea turtles, the presence of congenital malformations frequently leads to mortality. A few years ago, a detailed study was performed on external congenital malformations in three species of sea turtles from the Mexican Pacific and Caribbean coasts, the hawksbill turtle, Eretmochelys imbricata (n = 23,559 eggs), the green turtle, Chelonia mydas (n = 17,690 eggs), and the olive ridley, Lepidochelys olivacea (n = 20,257 eggs), finding 63 types of congenital malformations, of which 38 were new reports. Of the three species, the olive ridley showed a higher incidence of severe anomalies in the craniofacial region (49%), indicating alterations of early developmental pathways; however, several malformations were also observed in the body, including defects in the carapace (45%) and limbs (33%), as well as pigmentation disorders (20%), indicating that deviations occurred during the middle and later stages of development. Although intrinsic factors (i.e., genetic mutations or epigenetic modifications) are difficult to monitor in the field, some environmental factors (such as the incubation temperature, humidity, and probably the status of feeding areas) are, to some extent, less difficult to monitor and/or control. In this review, we describe the aetiology of different malformations observed in sea turtle embryos, and provide some actions that can reduce embryonic mortality.