Congenital Mullerian anomalies are rare developmental defects that result in malformation of the fallopian tubes, uterus, cervix, and vagina. The bicornuate uterus is one of the many variants of Mullerian anomalies, defined as having an external fundal indentation of greater than one centimeter. Pelvic ultrasound has a sensitivity of 99% for identifying bicornuate uteruses and is the predominant imaging device used for diagnosis. The cervical and uterine cavity anatomy in patients with a bicornuate uterus varies. The effect of maternal uterine structure on offspring development has been poorly documented. This report details a rare case of dichorionic-diamniotic twin pregnancy in a bicornuate uterus with one fetus affected by Ebstein’s anomaly. Twin A was diagnosed by first-trimester ultrasound with right renal agenesis and Ebstein’s anomaly. Twin B did not have any anatomical defects identified on ultrasound. Both twins were delivered via emergency repeat cesarean section at 34 weeks and four days due to nonreassuring fetal heart tracings and twin A in the breech presentation. Twin A and twin B were found to be in separate horns within the uterus during low transverse cesarean section. Twin A required endotracheal intubation in the delivery room due to respiratory distress. Both twins required neonatal intensive care treatment. Twin A was found to have a right pelvic kidney, rather than right renal agenesis, while in the neonatal intensive care unit. Females with germline mutations in the Mullerian duct and urogenital sinus development have resulted in concomitant malformations in the uterus and kidneys. This is a rare case of an infant with a cardiac anomaly born to a mother with a germline mutation. The relationship between congenital heart defects and uterine anomalies has not been identified. As seen in this case, maternal malformations impacting fetal cardiac development can be sporadic or result from germline mutations in mesoderm that have not been reported yet.