Our aim was to find out the prevalence of oral clefts in Madagascar, to compare it with elsewhere in the world, and to give the possible cause of the particular rate in the Vakinankaratra region where Antsirabe is situated. Data were collected from birth registers from 1998 to 2007 in the 10 most important hospitals of the 6 former provinces and of Antsirabe. A total of 150,973 consecutive live births were recorded in the 6 provinces, and 175,981 including those from Antsirabe. The general birth prevalence of oral clefts was 0.48‰ (about 1/2100, n=150,973) which was made up of 0.23‰, 0.12‰, and 0.11‰ for cleft lip and palate, isolated cleft lip, and isolated cleft palate, respectively. Prevalence was greater on the Central Highlands than in the coastal regions. Higher prevalence rates were found among girls than boys (64.4% compared with 35.6%, p<0.01). Of the clefts, 65.5% were unilateral, and left-sided ones were most common (77.8%). If the results obtained in Antsirabe are also considered, birth prevalence of oral clefts was 0.92‰ (about 1/1100, n=175,981) if Antsirabe is included, and 0.41-0.50‰ in the 6 former provinces; rates of associated, or syndromic, forms, or both, were 21.9% in the 6 provinces and 26.1% in Antsirabe. Overall, the prevalence of oral clefts in Madagascar does not differ from that in the rest of the world, except for the sex difference. There was a high prevalence of oral clefts in general and associated or syndromic forms, or both, in the Vakinankaratra region. There may be a link between these results and background high doses of ionising radiation in some areas because of the presence of former uranium mines. Further research is needed to obtain more precise data.