The aims of this study were to determine the frequency of the Ponticulus posticus (PP) in the C1 vertebra and the Sella Turcica Bridge (STB) and Clinoid enlargement (CLEN) variants in two samples of Peruvian cleft lip and palate patients (CLP), determine if there are significant differences between sexes and compare the results with two samples of non-cleft controls. The digital images of the lateral cephalometric radiography of 163 and 150 CLP patients were utilized to determine the frequency of PP and, STBCLEN respectively. The controls were composed of 1056 and 417 radiography of non-cleft patients. The chi-square statistic was utilized to determine if there were significant differences between genres for the CLP patients, and between the CLP and control samples. The confidence level was set at p<0.05. The frequency of PP (partial and complete) in CLP patients was 11.04% (18 cases) and 6.13% (10 cases) respectively; both of them were more frequent in males and there were no significant differences between sexes and between the CLP and control groups (p>0.05). The frequency of STB and CLEN in CLP patients was 6% (9 cases) and 8.7% (13 cases) respectively; both of them were more frequent in males and there were no significant differences between sexes and between the CLP and control samples for the STB (p>0.05). The frequency of CLEN was significantly lower (p<0.05) in the cleft group and in the female cleft group when compared to the control group. The frequencies of the Ponticulus Posticus, Sella Turcica Bridge and Clinoid Enlargement were similar to the control group and should not be considered as Cleft Lip and Palate associated anomalies; the frequency of the Clinoid Enlargement was significantly lower in cleft patients and this could be confirmed through studies centered on the Clinoid apophysis.