The objectives of this retrospective study of 240 guinea pigs (148 females and 92 males) were to determine the prevalence of different vertebral formulae and the type and anatomical localization of congenital vertebral anomalies (CVA). Radiographs of the cervical (C), thoracic (Th), lumbar (L), sacral (S), and caudal (Cd) part of the vertebral column were reviewed. Morphology and number of vertebrae in each segment of the vertebral column and type and localization of CVA were recorded. In 210/240 guinea pigs (87.50%) with normal vertebral morphology, nine vertebral formulae were found with constant number of C but variable number of Th, L, and S vertebrae: C7/Th13/L6/S4/Cd5-7 (75%), C7/Th13/L6/S3/Cd6-7 (4.17%), C7/Th13/L5/S4/Cd6-7 (2.50%), C7/Th13/L6/S5/Cd5-6 (1.67%), C7/Th12/L6/S4/Cd6 (1.25%), C7/Th13/L7/S4/Cd6 (1.25%), C7/Th13/L7/S3/Cd6-7 (0.83%), C7/Th12/L7/S4/Cd5 (0.42%), C7/Th13/L5/S5/Cd7 (0.42%). CVA were found in 30/240 (12.5%) of guinea pigs, mostly as a transitional vertebra (28/30), which represents 100% of single CVA localised in cervicothoracic (n = 1), thoracolumbar (n = 22) and lumbosacral segments (n = 5). Five morphological variants of thoracolumbar transitional vertebrae (TTV) were identified. Two (2/30) guinea pigs had a combination of CVA: cervical block vertebra and TTV (n = 1) and TTV and lumbosacral transitional vertebra (LTV) (n = 1). These findings suggest that guinea pigs’ vertebral column displays more morphological variants with occasional CVA predominantly transitional vertebrae.