Fanconi anemia (FA) is a rare autosomal recessive inherited disease caused by gene mutations that are primarily involved in the response to or repair of DNA damage. FA characterizes by multiple congenital abnormalities and malformations including growth retardation, renal agenesis, absence of radial bones and thumbs as well, progressive bone marrow failure, irregular skin pigmentation patterns, and increased susceptibility to cancer. FANCD2 gene mutation is believed to be one of the causative mutations in Fanconi anemia, and despite many case reports that link the FANC gene mutation to multiple congenital anomalies and disease, there is no case report found to link it with genitalia abnormalities. In our paper, we report a male Saudi infant who presented to the endocrine clinic at the age of 9 months with severe ambiguous genitalia and found that he carries a homozygous variant mutation in the FANCD2 gene and we face a challenge to treat this patient since there was no previous similar case.