Amniote egg and eggshell morphology is a rich source of characters to link aspects of reproductive biology with systematics. Extensive work concerning both anatomy and phylogenetic assignability has been done on fossil bird and dinosaur eggs, but little is known for extant sauropsids. The utility of eggshell characters for phylogenetic analyses is tested and discussed for extant side-necked turtles (Pleurodira), and the diversity of egg ultrastructure is examined in several species. Egg gross morphology and eggshell ultrastructure of 12 species of extant side-necked turtles was documented using scanning electron microscopy. Thirteen eggshell characters were scored and mapped on a composite phylogeny and ancestral character states were reconstructed. Many of the characters do not show a phylogenetic signal according to a test comparing the number of steps on the chosen phylogeny with that on randomly generated trees. The presence of conservative, clade-supporting features could be demonstrated, and the following clades are supported by several characters: the Elseya-Emydura entity, short-necked Australasian chelids, is backed by two characters, and two additional characters could potentially support this group. Three characters support the monophyly of South American chelids, whereas two characters argue for the exclusion of Hydromedusa, a long-necked form resembling Australian chelids rather than South American forms, from this clade.