A long-standing question regarding the evolution of the snake body plan is to what extent does axial regionalization and organ position correspond with that of generalized tetrapod vertebrates. Here, we evaluated the position of shifts in vertebral morphology with respect to heart location in 2 species and 13 specimens of garter snakes (Thamnophis). From dissections, geometric morphometrics, and segmented regressions on principal component scores describing shape of the cranial aspect of vertebrae, we determined a consistent morphological transition at approximately 17% of the pre-cloacal vertebral column. The transition was strongly coincident with the position of the heart, suggesting a developmental link between the first major transition in vertebral regions and the longitudinal position of the heart in garter snakes. Our novel discovery has implications for further recognizing the pre-cloacal vertebral column of snakes as regionalized, and that these regions are positionally linked with organogenesis of the viscera.