Deletion of distal portion of short of chromosome 3 and duplication of short-arm of chromosome17 are rare genetic disorders. There are no case supports in literature where a deletion of chromosome 3p or duplication of chromosome 17p has been reported with esophageal atresia/ tracheo esophageal fistula. Our index patient had no family history of any genetic abnormalities. We are reporting an infant with esophageal atresia, tracheoesophageal fistula, intrauterine growth retardation, cryptorchidism, hypospadias and sacral abnormality with deletion of 3p26.3 and duplication of 17p13.3. The clinical presentation is generally associated low birth weight, growth retardation, mental retardation, facial dysmorphism. Duplication of 17 P 13.3 has been reported to be associated with facial dysmorphism, corpus callosum hypoplasia, cerebellar hypoplasia and moderate mental retardation. Deletion of chromosome 3 could be familial or de novo.