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To identify the long-term effects of clefts (intrinsic and functional) on craniofacial growth and to evaluate the possible association between the sizes of the cleft maxillary segment (intrinsic) and alveolar cleft (functional) and the craniofacial morphology in patients with unilateral cleft lip and palate (UCLP).Retrospective case-control study.Sri Lankan Cleft Lip and Palate Project.Thirty unoperated adult patients with UCLP and 52 normal controls.Maxillary dental cast was used to measure the sizes of the cleft maxillary segment and alveolar cleft. Cephalometry was used to determine craniofacial morphology.Patients with UCLP had shorter height of the basal maxilla, shorter posterior length of the basal maxilla, and less protruded basal maxilla at the zygomatic level than did control subjects. In patients with UCLP, the posterior height of the basal maxilla was related to the size of the cleft maxillary segment, and there was a tendency toward significant association between the anterior height of the basal maxilla and the size of the alveolar cleft.The adverse effects of clefts on the growth of the maxilla in patients with UCLP are restricted to the basal maxilla in size. This growth inhibition is major in height and minor in length. The reduced posterior height of the basal maxilla in unoperated patients with UCLP might be primarily attributed to intrinsic effects, whereas the reduced anterior height of the basal maxilla might be attributed to functional effects.