Congenital malformations of the female genital tract are defined as deviations from normal anatomy. They are due to embryological maldevelopment of the Mullerian or paramesonephric ducts. Septate uterus is the most common of all Mullerian duct defects. A rare case of a viable twin pregnancy in separate components of a septate uterus is reported. The diagnosis of uterine malformation was made before pregnancy. The viability of the twin gestation was detected and confirmed by transabdominal and transvaginal sonography. Moreover, the location of the fetuses was confirmed by a magnetic resonance imaging (MRI). A specific schedule of prenatal screening was provided. Two healthy neonates were delivered by a cesarean section in the 34^th week of gestation. The importance of MRI and management of this high-risk pregnancy is discussed.