The rate of malformations and major medical conditions in early childhood was analyzed in a single village according to the degree of relationship between the parents. In the village, 70-80% of the marriages are between descendants of the founders and therefore consanguineous. In the period 1992-2003, in 99 of 2,610 children, a major malformation was diagnosed at birth and seven additional fetuses were aborted because of a severe malformation. A significant medical condition was diagnosed in 38 additional children in early childhood. The total of 144 cases with malformations or a major medical condition represented 5.52% (95% CI: 4.64-6.4) of the live births. Three malformations/disorders were relatively frequent: Down syndrome, esophageal atresia, and profound deafness. The rate of malformations and significant medical conditions was 7.77% (95 CI: 5.68-9.86) when the parents were first cousins and 3.63% (95% CI: 2.11-5.15) when they were not related (P = 0.002, Fisher's exact test). Offspring of parents that were second cousins or closer but less than first cousin had a risk that was similar to the one of offspring of couples that were more distantly related. We propose therefore, that in inbred populations, all the couples that are not related as first cousins but in which the spouses are both descendants of the founders should be considered as related. The high prevalence of profound deafness in the village is due to mutations in the Connexin 26 gene, while the relatively high frequency of Down syndrome is not explained by maternal age only.