Patients with Fanconi's Anemia (FA) have high rates of congenital physical abnormalities, bone marrow failure, leukemia, and solid tumors. Stem cell transplant (SCT) is often effective in curing bone marrow failure, but high-risk patients, particularly those whose donor is not a human leukocyte antigen matched sibling, are vulnerable to early mortality from transplant-related complications. Long-term survivors of SCT have risks of solid tumors (particularly of the oral cavity), which are even higher than the already high 'baseline' risk of neoplasia in untransplanted FA patients. In this group, the major types of cancer are head and neck squamous cell carcinomas, and gynecologic malignancies. Rapid evaluation of new SCT preparative regimens would be useful in improving both short-term and long-term results.