Cleft lip and/or palate (CL/P) are the most common craniofacial abnormalities. CL/P therapy involves also orthopedic and surgical treatments. In particular, the orthopedic treatment can help to align the cleft segments and facilitate surgery. Traditionally, facial and palatal structures have been analyzed by 2D methods, omitting information of volume bone defects. A pre-surgical volume estimation can be useful to determine the anatomical boundaries of the alveolar bone defect; subsequently, volume assessments can appreciate the outcome of secondary alveolar bone grafting. In the present study, we developed a 3D stereophotogrammetric technique for volume estimation of the dental arches of children with CL/P. The method was employed to assess the 3D changes occurring in the maxillary arch of unilateral CLP (UCLP) patients with the use of plates before the first year of life. We collected 96 palatal casts of 32 neonatal patients with UCLP. Palatal casts were obtained before orthopedic treatment, before cheiloplasty, and after cheiloplasty. Half patients were treated with an active plate, half with a passive one. Casts were marked with a set of landmarks, digitized using a stereophotogrammetric system, and then analyzed. Volumes of the greater and the minor alveolar segments were separately assessed, and compared with a 3-w repeated measures ANOVA. Method accuracy was assessed using objects of known size, while repeatability was evaluated using Student's t test and technical error of measurements. Volume estimates were accurate, without systematic errors; random errors were lower than 5% of the total variance. Significant effects of alveolar segment and time were observed (p<0.0001). Instead, no differences were found for the kind of plate. In conclusion, stereophotogrammetric systems can be a valid instrument to estimate palatal volumes of patients with CL/P during treatment, that can be followed up in a safe, rapid and non-invasive way.