Snakes are an extremely modified and long-lived clade of lizards that have either lost or highly altered many of the synapomorphies that would clearly link them to their closest sister-group among squamates. We focus here on one postcranial morphological complex, the intercentrum system which in most non-ophidian squamates is limited to the cervical and caudal regions. The Cervical Intercentrum System (CeIS) is composed of a single intercentral element that sometimes articulates with a ventral projection (hypapophyses) of the centrum; the Caudal Intercentrum System (CaIS) is formed by an intercentral element, the haemal arch/chevron bone, and paired ventral projections of the centrum, the haemapophyses. In modern snakes, the intercentrum element of the CeIS is considered lost or fused to the hypaphophysis, and the chevron bone in CaIS is considered lost. Here, we describe new specimens of the early snake Dinilysia patagonica, and reinterpret previously known specimens of Dinilysia and Najash rionegrina, that do not show the expected snake morphology. The anatomy of these fossil taxa unambiguously shows that free cervical and caudal intercentra attached to distinct downgrowths (hypapophyses and haemapophyses) of the centra, are present in basal fossil snakes, and agrees with the proposed loss of post atlas-axis intercentra in later evolving snakes.