Squamata (amphisbaenians, “lizards”, mosasaurs, and snakes) is an extremely diverse clade with a rich fossil record. There is little consensus about the interrelationships of the major squamate clades (i.e., Iguania, Gekkota, Scincomorpha, Anguimorpha, Amphisbaenia, and Serpentes), or even the membership of some of these clades. Morphology-based cladistic analyses typically agree only that the major dichotomy in extant squamates is between Iguania and all other taxa. The phylogenetic placement of Amphisbaenia and Serpentes is particularly problematic. Incomplete taxon sampling is likely a major contributing factor to the absence of a consensus about squamate interrelationships. This study examines squamate relationships using 222 ingroup taxa scored for 363 morphological characters. Analysis of these data recovered 2,213 equally short trees with a length of 3,273 steps and a retention index of 0.7164. The results confirm the monophyly of the clades Scleroglossa (extant squamates exclusive of Iguania), Gekkota, Scincomorpha, Lacertoidea, Scincoidea, Anguimorpha, Carusioidea, Platynota, and Varanoidea. Novel results include the identification of a clade containing Scincidae sensu lato, Dibamidae, Amphisbaenia, and Serpentes; identification of a Mesozoic clade containing Bainguis, Eoxanta lacertifrons, Globaura venusta, and Myrmecodaptria; and identification of Dalinghosaurus as a basal shinisaur. A new taxonomic scheme is outlined. The names Iguanomorpha, Scincogekkonomorpha, Evansauria, and Mosasauriformes are applied to the stem-based groups including Iguania, Scleroglossa, Autarchoglossa, and Mosasauria, respectively. The importance of strict rigidity within taxonomy is questioned; taxonomy is most useful as a tool for communication about organisms or groups of organisms.