We report a case of a fetus with shortened proximal long bones, ambiguous genitalia, intrauterine growth restriction and abnormal umbilical artery Doppler velocities observed on antenatal ultrasound exam. At 34 weeks the patient revealed methotrexate/misoprostol exposure at 6 weeks gestational age in attempted medical termination of pregnancy. On newborn exam, the baby had dysmorphic facial features, a short torso, scoliosis, a micropenis (phallus <1cm) and shortened proximal long bones both upper and lower extremities. X-ray exam revealed a hemivertebra at T10 level, rib abnormalities, shortened proximal long bones, an absent pubic bone and bilateral knee ossification centers. With methotrexate exposure, improved counseling and surveillance could potentially avoid these significant abnormalities and prevent psychological distress.