Among rabbits and guinea pigs, dental problems are the most common reason for performing cranial computed tomography (CT). This investigation reviewed CT scans of both species to determine the nature and frequency of lesions arising from dental disorders. Head CT data from 48 rabbits and 52 guinea pigs diagnosed with dental abnormalities were retrospectively examined. Pathologies involving mandibular teeth predominated, seen in 81.2% of rabbits and 98% of guinea pigs. In rabbits, aggressive osseous reactions adjacent to affected teeth were the main mandibular and maxillary changes, whereas in guinea pigs, peri-root swelling with focal bone loss in the maxilla, and thickening without lysis in the mandible, were more typical. Nasal cavity hyperattenuation—indicative of rhinitis—was the most common maxillary alteration in both rabbits (60%) and guinea pigs (83.3%), while exophthalmos occurred more often in rabbits (53.3%). In the mandibular region, space-occupying cavernous lesions appeared most frequently in rabbits (92.3%) and guinea pigs (73.3%). Dental-related secondary lesions were frequently encountered in both animals, confirming the diagnostic usefulness of CT for recognizing associated cranial and soft tissue alterations.