Premature ovarian failure (POF), that is, amenorrhea before 40 years of age can be attributed to a variety of etiologies. Approximately 1% of women before 30 years are diagnosed with POF. Spontaneous ovulation leading to pregnancy in POF is even a rarer entity. We report a case where congenital malformations were diagnosed in a fetus following spontaneous ovulation in a case of POF. A 33-year-old woman presented to our center with primary infertility. On complete work up, she was diagnosed with POF and conceived with hormone replacement therapy and donor oocyte program. She delivered a healthy female baby through caesarean section. The patient reviewed later with amenorrhea of 40 days and pregnancy was confirmed. However, during antenatal follow-up congenital anomalies in fetus were diagnosed sonographically. The decision for termination of pregnancy was taken. To conclude, we recommend large-scale retrospective analysis that would define medical guidelines in cases of pregnancy following spontaneous ovulation in POF.