Background: Concepts regarding cleft lip and palate care vary widely globally, as there is no international consensus. Consequently, institutional surveillance of cleft concepts is essential. In addition to subjective expert rankings, three-dimensional (3D) photogrammetry of the face has become the gold standard for evaluation and objective assessment of facial structures. We evaluated cleft configuration preoperatively to determine the influence thereof on the long-term facial appearance/averageness of unilateral cleft lip patients. Methods: Plaster models of the patient's labio-oral region and nose were made preoperatively, digitized, and cleft configuration assessed (cleft width, cleft-columella angle, nasal projection, heminasal width ratio, transverse lip length, labial height). Between 4 and 12 years after surgery, stereophotogrammetry (3D face scans) were captured to determine the patients' individual facial averageness index (FAI) as a deviation from the population mean, using proportion indices (PIs) of facial landmarks and reference data provided by Farkas and FaceBase. Results: Cleft width (r = 0.77) and columella length correlated strongly with long-term facial averageness (r = 0.52). Decreasing FAI was seen with increasing patient age (r = -0.42), indicating increasing facial averageness. Other cleft properties showed weaker correlations. Cleft alveolus did not have any impact on FAI. Conclusions: The presented method allows objective measurement of facial appearance/averageness as well as preoperative cleft properties. It might be superior to subjective assessments of facial attractiveness/appearance. Objective cleft measurements are strong predictors for future facial averageness. Increasing averageness with growth and age suggests late corrective surgery.