Purpose The main aim of the present study was to investigate the dimensions and morphological appearance of the sella turcica in cleft lip and palate patients using cone-beam computed tomography (CBCT) images, compared to non-cleft individuals. Methods CBCT images of 40 (20 females and 20 males) cleft lip and palate patients and 60 (27 males and 33 females) non-cleft individuals were assessed, retrospectively. The linear dimensions (depth, diameter and length) of the sella turcica and inter-clinoid distance were measured. Sella turcica shapes were examined in the cleft lip and palate patients and non-cleft individuals. Non-cleft individuals were divided into skeletal malocclusion classes. All variables were analyzed using the Kruskal-Wallis test, Mann-Whitney U tests and Chi-square test. Results No significant difference was observed between individuals with and without cleft in the linear dimensions (depth, diameter and length) of the sella turcica (p > 0.05). However, a significant difference was found in the inter-clinoid distance between patients with cleft and non-cleft individuals (p < 0.05). Comparison of the sella turcica shape between skeletal malocclusion classes and patients with cleft showed significant differences (p < 0.05). Conclusions No significant difference was determined in the depth, diameter, or length of the sella turcica in cleft patients when compared with non-cleft individuals. The inter-clinoid distance was lower in cleft patients than in non-cleft individuals, and this difference was statistically significant.