Background Stereophotogrammetry can be used to study facial morphology in both healthy individuals as well as subjects with orofacial clefts because it shows good reliability, ability to capture images rapidly, archival capabilities, and high resolution, and does not require ionizing radiation. This study aimed to compare the three-dimensional (3D) facial morphology of infants born with unilateral cleft lip and palate (UCLP) with an age-matched normative 3D average face before and after primary closure of the lip and soft palate. Methods Thirty infants with a non-syndromic complete unilateral cleft lip, alveolus, and palate participated in the study. Three-dimensional images were acquired at 3, 6, 9, and 12 months of age. All subjects were treated according to the primary surgical protocol consisting of surgical closure of the lip and the soft palate at 6 months of age. Three-dimensional images of UCLP patients at 3, 6 (pre-treatment), 9, and 12 months of age were superimposed on normative datasets of average facial morphology using the children’s reference frame. Distance maps of the complete 3D facial surface and the nose, upper lip, chin, forehead, and cheek regions were developed. Results Assessments of the facial morphology of UCLP and control subjects by using color-distance maps showed large differences in the upper lip region at the location of the cleft defect and an asymmetry at the nostrils at 3 and 6 months of age. At 9 months of age, the labial symmetry was completely restored although the tip of the nose towards the unaffected side showed some remnant asymmetry. At 12 months of age, the symmetry of the nose improved, with only some remnant asymmetry noted on both sides of the nasal tip. At all ages, the mandibular and chin regions of the UCLP patients were 2.5–5 mm posterior to those in the average controls. Conclusion In patients with UCLP deviations from the normative average 3D facial morphology of age-matched control subjects existed for the upper lip, nose, and even the forehead before lip and soft palate closure was performed. Compared to the controls symmetry in the upper lip was restored, and the shape of the upper lip showed less variation after primary lip and soft palate closure. At this early age, retrusion of the soft-tissue mandible and chin, however, seems to be developing already.