Nasal septum deviation is one the most significant nasal deformities among cleft and lip patients and its anatomical variations along the anterior-posterior axis within the nasal cavity has not been specified. To define whether there are differences in the degree of nasal septum deviation between the anterior, middle and posterior areas of the nasal cavity in operated unilateral cleft lip and palate patients. Twenty-nine unilateral complete cleft lip and palate patients, between 5 and 17 years, attending San Borja Arriarán Hospital and the University of Chile's School of Dentistry were included. The nasal septum deviation index was measured at different depths across the anteroposterior axis by cone-beam computed tomography. A random effects model was performed for data analysis. The nasal septum deviation index presented differences between the three planes studied. The plane with lesser deviation was the anterior, while the plane with greater deviation was the posterior. These differences resulted statistically significant (P < 0.05). In complete unilateral cleft and lip patients mainly the posterior part of the nasal septum should be corrected, because there is a greater deviation in that area.