Two groups of scientists recently reevaluated specimens of a fossil snake from 98 million year old sediments of the Middle East, arriving at different conclusions regarding its genetic relationships and sparking an ongoing debate involving the origins and the evolutionary history of snakes. One group that Pachyrhachis was primitive and regarded it as intermediate between lizards and snakes. The other group found it more closely related to pythons and boa constrictors, and, therefore, a relatively evolved snake. Understanding the relationships of Pachyrhachis problematicus relies on a clear understanding of the morphology of its skull. Two specimens of Pachyrhachis exist; one preserves a disarticulated skull crushed beneath the rib cage and the other preserves a nearly complete and articulated but crushed skull. The dorsal surface of the skull of the articulated specimen was embedded in epoxy resin for acid removal of limestone during its original study nearly 30 years ago. The resin is cloudy, and the glass covering the epoxy surface was broken at some point, rendering it difficult to view the dorsal surface using microscopes or the naked eye. Therefore, both groups of investigators made their observations of relevant morphology under less than ideal conditions. This study employs CT scanning and three-dimensional computer generated reconstructions to reassess the morphology of Pachyrhachis, providing an independent test of previous observations and, thus, a basis for choosing between the competing hypotheses. Pachyrhachis is confirmed as a derived snake allied with boas and pythons.