In wild populations negative effects from inbreeding are usually difficult to assess. The contemporary Scandinavian wolf population (Canis lupus) was established in 1983. With only three founders this population, with approximately 100 individuals, exhibits lower genetic variability than the neighbouring eastern population. Congenital malformations of the backbone were found in this highly inbred population. This study assesses the frequency and morphology of vertebral malformations within the Scandinavian wolf population and compares this with two reference populations. We discuss the etiology of malformations, how they may affect individuals and viability for the population. The frequencies of lumbosacral transitional vertebrae were higher in the small contemporary population than in the eastern reference population. Certain other defects were not found in the reference populations. This study demonstrates malformations that may have a negative impact on the Scandinavian wolf population and be an indication of inbreeding depression. For the conservation of this endangered population, we assert that immigration of wolves from eastern populations is essential.