Assessment of surgical outcome in congenital craniofacial malformations is necessary to evaluate treatment efficiency since the results of early surgery are influenced by surgical technique and timing. Available outcome measurements all have their limitations, especially for application in congenital craniofacial malformations. Therefore a new outcome measurement was developed, in which each facial unit is scored in a standardized way. For each facial unit, deformities of shape or contour, malposition and soft tissue involvement were evaluated, besides scoring for specific congenital malformations of that area. The final result was tested on pre- and postoperative photographs of patients with rare facial clefts and reliability and validity were demonstrated. The new developed instrument showed the ability to provide quantification of outcome. Because of its properties it can serve as an instrument to compare outcome between techniques, surgeons and centers in a more objective and standardized way.