High-resolution computed tomography provides an alternative to serial sectioning and other destructive techniques of studying fossils (data available at http://www.DigiMorph.org). This technology was used to study the oldest aistopod Lethiscus stocki. The fossil is found to have approximately 30 closely spaced teeth on its maxilla and dentary, a short vomer, a palatine running nearly the entire length of the maxilla that is toothed at least posteriorly, and a choana that is located at the premaxilla–maxilla suture. It has a lower jaw with a high articlular facet for the quadrate condyle; a lateral fossa for the adductor musculature, superficially similar to the mammalian masseteric fossa; and a sutural pattern that closely resembles that of Oestocephalus. Previously reported pectoral elements are not evident in the scans and may be best interpreted as fractures on the surface of the nodule associated with sedimentary inclusions. Relationships among all relatively complete aistopods were analyzed using parsimony. Two most parsimonious trees were found, differing in the arrangement of the outgroup taxa. Phlegethontia and Pseudophlegethontia are found to be sister taxa to Coloraderpeton and Oestocephalus,with Ophiderpeton and Lethiscus placed as successively more distant taxa. This topology renders Ophiderpetontidae, as previously conceived, paraphyletic. Lethiscus is confirmed to be the most basal aistopod. A new classification of Aistopoda is presented. This study shows that the palatoquadrate of higher aistopods is derived in-group, which is consistent with the trends in aistopods of peramorphosis in the endochondral skeleton and paedomorphosis in the dermal skeleton.