In vitro production and somatic cell nuclear transfer are biotechnologies widely used for breeding cattle, although may result in congenital anomalies. This paper aims to report a set of congenital anomalies in two Nelore calves, a male and a female, produced through in vitro fertilization. The major anomalies revealed at necropsy were hypospadias, bifid scrotum, atresia ani and rectum ending in blind pouch in the male calf. In the female calf accessory spleen, atresia ani, underdevelopment of extern genitalia and urethral orifice, and rectum ending in blind pouch forming a uterus-rectum fistula were observed.