At least 26 lineages of snakes and lizards have independently evolved the elongate, limbless body plan most well known in snakes. Elongation is always a feature in this transition and precedes limb loss, yet which body regions contribute most to elongation has been difficult to discern. This is largely because in elongate species, there is a breakdown in the boundary between the neck and trunk regions. In limbed species, this boundary is defined by the location of the sternum, and there are certain features that all occur at this boundary (e.g. limbs, vertebral characters). But many elongate species lack limbs and even sterna, and other neck-trunk boundary characters become displaced relative to each other during the evolution of limblessness. This has caused confusion about where the neck-trunk boundary is in elongate species, as it is difficult to determine what character should define the boundary when limbs and sterna are absent. To bring clarity to this issue, CT data from limbless taxa across Squamata and closely related outgroups were examined to determine the axial positions of various neck-trunk boundary markers such as the pectoral girdle, the posterior extent of cervical vertebral characters, and overall vertebral shape as determined by a geometric morphometric analysis. Results suggest that, generally, the position of the pectoral girdle is the most conserved, and cervical characters such as hypapophyses are the most posteriorly displaced, compared to the plesiomorphic body plan. In elongate species with highly reduced pectoral girdles, the boundary as determined by any vertebral character does not coincide with the position of the pectoral girdle, meaning vertebral characters may not be a reliable indicator of where the traditionally defined neck-trunk boundary would have been in species without pectoral elements.