Additional congenital anomalies have often been found in patients with orofacial clefts. We wanted to find out the incidence and type of congenital malformations that may accompany cleft palate (CP) and cleft lip and palate (CLP) in babies born in the Konya region. A total of 121 newborn babies with CP or CLP were prospectively included in the study, and all were assessed in detail for congenital anomalies. Of 121 babies, 86 (71%) had CLP and 35 (29%) had CP. There was at least one congenital malformation in 80 (66%) of the cases. Additional congenital malformations were seen in 26 (74%) of the 35 with isolated CP, and 54 (63%) in the 86 patients with CLP (p < 0.05). The most common congenital malformation was congenital heart disease, followed by head and neck anomalies. The most common congenital heart disease was atrial septal defect. A serious chromosomal anomaly was found in 18/121 patients with CP or CLP (15%). Of the 80 babies in whom congenital malformations were found, 31 (39%) had dysmorphic features. While 21 (68%) of dysmorphic cases had isolated CP, 10 (32%) had CLP (p < 0.05). The rates of premature delivery, intrauterine growth retardation, and consanguinity between parents were higher in patients with CP or CLP. The neonatal mortality was 20% (n = 24). Our results indicate that at least one congenital anomaly is also present in about two-thirds of newborn babies with CP and CLP, and these anomalies significantly increase their morbidity and mortality. All newborn babies with CP and CLP should be screened for additional congenital anomalies, particularly of the cardiovascular system. © 2011 The British Association of Oral and Maxillofacial Surgeons.