Two egg types from the Upper Cretaceous Two Medicine Formation of Montana are described and incorporated into a phylogenetic analysis of egg characters. Small (7.5 × 3.5 cm), ellipsoidal eggs with a surface ornamentation consisting of isolated round tubercles represent a new, unnamed ootaxon. The microstructure includes narrow, prismatic shell units with three structural layers. The second egg type, oospecies Prismatoolithus levis, belongs to the theropod Troodon formosus. Although previously described, the presence of a third, external layer had been overlooked. Both eggs display several features typical of avian eggs: narrowly spaced nucleation sites, barrel-shaped mammillae with blocky crystal habit, a squamatic-like texture in the prismatic layer, and a third, structural layer. In addition, the new egg type exhibits a cuticle layer and the eggs of Troodon are asymmetric.Cladistic analysis of 14 fossil and extant taxa using 15 egg and shell characters favors a phylogeny consistent with more traditional analyses based on osteologic or genetic data and supports a theropod dinosaur origin for birds. No single character unambiguously distinguishes the eggs of avians from those of non-avian theropods, and the new Two Medicine egg type is recognized simply as that of a theropod. Results also indicate that resemblances in egg characters among non-avian and avian theropods are largely homologous and imply a high-level of similarity in reproductive physiology. Egg features are phylogenetically informative; better classifications and greater utility of eggs and eggshell will be gained through their phylogenetic treatment.