The usefulness of three-dimensional (3D) stereophotogrammetry for treating cleft lip (CL) has been well documented. However, there are only a few reliable anthropometric analyses in infants with CL because at this age they cannot assume a resting facial position. Since 2014, we have used a handheld 3D imaging system in the operating room to obtain optimal images of infants with CL and palate under general anesthesia. Currently, 168 infants with a unilateral cleft, 50 infants with bilateral clefts, and 47 infants with an isolated cleft palate are being followed up in this way for a maximum of 30 months. Most patients ≥3 years of age are cooperative and allow staff to obtain 3D images without sedation. We plan to follow them until adulthood, obtaining 3D images at every intervention. Each year, >150 infants can be added to this ongoing longitudinal study. Using an archive of these digital images, various retrospective studies can be attempted in the future, which include comparisons of the long-term outcomes of various surgical techniques and interventions at different time intervals. This is the first 2-year preliminary report of a 20-year longitudinal study.