In the literature, there is an abundance of promising data on the outcome of allogeneic stem cell transplantation (SCT) in patients with Fanconi anemia (FA); however, the data on the outcome of FA patients who present with myelodysplasia and/or abnormal clone are sketchy as the entity itself is a rare one, although, it is believed that the presence of any of these factors confers a worse prognosis on the outcome of the transplant. This is an update of our experience in 11 such patients who underwent SCT at King Faisal Specialist Hospital and Research Center; 10 from the matched and related donors and 1 from a partially matched unrelated cord blood unit; the conditioning was with the same regimen consisting of cyclophosphamide (total of 20 mg/kg), anti-thymocyte globulin (total dose 160 mg/kg of the equine product or 52 mg/kg of the rabbit product) and total-body irradiation at 450 cGy. Ten patients remain currently alive, well and with no evidence of disease, with a median follow-up of almost 4 years.