The purpose of this study is to investigate the homology and polarity of enamel ultrastructural characters in the Multituberculata, one of the most evolutionarily successful radiations of early mammals. A number of recent studies have documented the morphological characteristics of enamel ultrastructure (variation in the shape, size, and spacing of “prisms”), however, little attempt has been made to analyze the results in a phylogenetic context. These studies have assumed that similar ultrastructural types are homologous to one another, and several have proposed that within multituberculates, small, circular prisms represent the primitive condition relative to large, arc-shaped prisms. We have tested these hypotheses by comparing the distribution of enamel ultrastructural types with a preliminary cladogram derived from an analysis of 22 characters of gross dental morphology for the most completely known Late Cretaceous and early Tertiary multituberculate genera (30 of 41 recognized genera). We conclude that each prism type is homologous in all multituberculates in which it occurs because of its consistency with non-ultrastructural characters used to construct the cladogram. A single exception to this consistent pattern exists, which we interpret as an instance of homoplasy. Neoliotomus has small, circular prisms rather than the large, arc-shaped prisms predicted by its location in the cladogram. Within Late Cretaceous and early Tertiary multituberculates, small, circular prisms are found only in relatively derived ptilodontoids (and Neoliotomus), whereas large, arc-shaped prisms are found in Paracimexomys, Cimexomys, cimolomyids (Meniscoessus and Cimolomys), the relatively primitive ptilodontoid Cimolodon, and all taeniolabidoids except Neoliotomus. The hypothesis that large, arc-shaped prisms represent the derived condition within multituberculates therefore should be rejected.