Caecilians are elongate, limbless and annulated amphibians that, as far as is known, all have an at least partly fossorial lifestyle. It has been suggested that elongate limbless vertebrates show little morphological differentiation throughout the postcranial skeleton. However, relatively few studies have explored the axial skeleton in limbless tetrapods. In this study, we used μCT data and three‐dimensional geometric morphometrics to explore regional differences in vertebral shape across a broad range of caecilian species. Our results highlight substantial differences in vertebral shape along the axial skeleton, with anterior vertebrae being short and bulky, whereas posterior vertebrae are more elongated. This study shows that despite being limbless, elongate tetrapods such as caecilians still show regional heterogeneity in the shape of individual vertebrae along the vertebral column. Further studies are needed, however, to understand the possible causes and functional consequences of the observed variation in vertebral shape in caecilians. It has been suggested that elongate limbless vertebrates show little morphological differentiation throughout the postcranial skeleton. However, our results show that, far from morphologically homogeneous, the post‐cranial skeleton of caecilians shows variations in vertebral shape. Whereas the anterior part of the body consists of short, bulky vertebrae, posterior vertebrae is elongated with pronounced basapophyseal processes.