The mode of inheritance of cleft lip with or without cleft palate (CL/P) has been extensively investigated, but the results are controversial. We report results of complex segregation analysis performed in the families of 636 consecutive newborns with CL/P registered in the northeast Italy and Emilia Romagna congenital malformation registries to test hypotheses regarding CL/P inheritance. The programs POINTER and COMDS have been used. POINTER could not distinguish between alternative genetic models, and only the hypothesis of no familial transmission could be rejected. COMDS results, after inclusion of the severity parameter, rejected the hypotheses of a single major locus and were consistent with the two-locus model with a major dominant locus and at least one modifier locus.