The reported survival of patients with Fanconi's anemia is highly varied, ranging from 2 to 25 years. The prognosis is especially poor if blood counts are low. Survival has likely been improved by the development and refinement of therapies, such as bone marrow transplantation.

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Although bone marrow transplantation can restore blood counts, patients with Fanconi's anemia remain predisposed to a variety of cancers (leukemia, myelodysplastic syndrome, liver cancer, and others).

Women with Fanconi's anemia who become pregnant should be watched carefully by a doctor, as they often require transfusions throughout pregnancy. Men with Fanconi's anemia have decreased fertility, although a small number have fathered children.