Children with cleft lip and/or cleft palate (CLP) often have additional congenital malformations. The reported incidences are variable and presumed underlying mechanisms are rarely discussed. In this study, 245 CLP patients of a geographically defined population were retrospectively reviewed for additional major malformations and minor anomalies. Malformation incidences in the CLP population were compared to those in a literature-based cohort from the general population. Of the CLP patients, 21% showed either major malformations or minor anomalies. In one-fifth of them a recognized syndrome was identified. Two thirds of the CLP patients with minor anomalies also had major malformations. Major malformations in non-syndromic CLP patients were found with decreasing frequency in the musculoskeletal (5.1%), central nervous (4.2%), urogenital (3.8%) and cardiovascular (3.4%) systems. Malformations in these organ systems and minor anomalies should be ruled out by a specialist. The rise in malformation incidence, when compared to the general population, was highest for organs of ectodermal and ecto-mesodermal origin: central nervous system (13 times), ocular (7 times) and craniofacial system (7 times). The result reflects the close interplay of craniofacial and brain development.