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The purpose of this study is to determine the prevalence of congenital heart disease in patients with cleft lip and/or palate. We undertook a retrospective study of 1148 cases, age < 15 years old, with cleft lip and/or palate from January 1991 to December 1998, of which congenital heart disease was associated in 62 patients. The overall prevalence of congenital heart disease in patients with clefts was 5.4%. Of the 62 patients, there were 38 boys and 24 girls. We classified clefts into one of three categories; group 1: cleft lip alone; group 2: cleft lip and palate; group 3: cleft palate alone. The cleft lip and palate (group 2) was present in the majority (27 of 62; 44%) of patients with congenital heart disease. Twenty-five patients (40%) had cleft palate, and ten patients (16%) had cleft lip. Isolated atrial septal defect and ventricular septal defect are the two common congenital defects, which presented 23% and 21% of patients, respectively. Apart from congenital heart disease and cleft lip or palate, 56% (35 of 62 patients) and additional abnormalities. Central nervous system and skeletal malformations were the most common associated abnormalities. In our study, congenital heart disease was more common in patients of group 2 and group 3 than of group 1. In addition, there was a significantly greater proportion of patients associated with other systemic anomalies in groups 2 and 3 than in group 1 (chi-square chi 2 = 7.535, p = 0.023), but no significant difference was noted between group 2 and group 3. We recommend that it would be appropriate for all cleft patients to receive a routine examination for associated anomalies by a pediatrician. With the widespread use of echocardiography and/or brain sonography, the early diagnosis and treatment of these anomalies are possible.