Objective: To evaluate the occurrence of cervical vertebrae anomalies (CVA) in patients with unilateral (UCLP) and bilateral cleft lip and palate (BCLP) using cone beam computed tomography (CBCT) examinations. Design: Retrospective assessment of CBCT images. Descriptive statistics were calculated. Fisher exact test or χ² test was performed to evaluate the differences among each CVA between sex and type of cleft. Setting: School of Dentistry. Participants: One hundred fifty-one patients with cleft lip and palate (103 UCLP/48 BCLP). Interventions: No relevant intervention. Main Outcome Measures: Cone beam computed tomography images were assessed for the presence or absence of 12 most commonly observed CVA: spina bifida, dehiscence, cleft of the posterior arch, cleft of the anterior arch, fusion between cervical vertebrae, block fusion, occipitalization, narrowing of the intervertebral space, posterior ponticle, os odontoideum, ossiculum terminale, and subdental cartilaginous remnants. Results: The presence of subdental cartilaginous remnants was the most frequently observed alteration—found in 81.45% of the sample—and it was the only CVA with statistically significant frequencies in the individuals with BCLP. Considering only the other CVA, 22.51% presented 1 and 5.29% presented 2 or more CVA. Conclusions: Patients with cleft lip and palate may present an overall high incidence of CVAs. However, when comparing the distribution of the CVAs among sex and types of cleft, the only significant difference noted was a higher incidence of subdental cartilaginous remnants among patients with BCLP.