The rate of gastro-intestinal tract atresia is around 0.3 percent in Georgia. In common cases delayed surgical treatment of these malformations is the reason of perinatal mortality. So, it is very important to concretize the risk factors, which cause the development of gastro-intestinal tract atresia. Our research was performed on the basis of examination of 161 probands with Gastro-Intestinal tract atresia and 155 control probands from the common population of Georgia, and also their relatives of I, II, III degrees of kinship. The methods of investigation were: clinical, paraclinical, genealogical, genetical-epidemiological. The analysis of the clinical material was done by the multiple-statistical method with the alternative analysis. It was shown, that an elderly age of parents, spontaneous abortions, or a hazard of spontaneous abortions, acute infections, emotional stress and the action of other teratogenic factors during the I trimester of pregnancy, hormonal misbalance of mother and some of the professional factors (especially agricultural) are most important etiologic and pathogenetic factors of the gastro-intestinal tract atresia.