Abstract The purpose of this retrospective case-control study was to compare the cephalometric features of parents of children with cleft anomalies to those of parents of normal children in the hope of finding potential markers of predisposition for this condition. There were 22 sets of parents of cleft children (study group) and 22 sets of parents of normal children (control group). A total of 88 lateral cephalograms were traced twice by two observers separately and analyzed using Student's t-test. Seven linear, two angular and five triangular cephalometric variables were measured. Mandibular body length (Go–Gn) in mothers was larger in the study than the control group, posterior cranial base (S-Ba) in fathers was shorter in the study than the control group, anterior maxillary triangle (S.N.A) in parents in the study group was larger than in the control group and posterior maxillary triangle (S.N.Pns) in study group mothers was larger than in control group mothers. In conclusion, the craniofacial morphology of the parents of children with cleft anomalies differs from that of parents of normal children and may have some predictive value.