Sex identification in young sea turtles is challenging. Sea turtle neonates lack external dimorphic characteristics and heteromorphic sex chromosomes. We compared the morphology of the gonads and reproductive ducts of dead formalin-preserved hatchling and post-hatchling Caretta caretta, Dermochelys coriacea, and Chelonia mydas and identified sex-specific differences in these structures that are useful in assigning sex. We tested 11 gross gonadal and reproductive duct characteristics in 57 neonate sea turtles and verified the sex by histological examination. A suite of four characters was found to reliably indicate sex in the three species considered: paramesonephric duct size, mobility of the duct, presence of a complete lumen and gonad mobility. Additionally, gonad shape and edge form were dependable sex-specific characters in cheloniids but not in D. coriacea. Together, these morphological characteristics provide new and reliable methods to quickly distinguish sex in preserved neonate sea turtles without using more extensive histological methods.