Fanconi Anemia patients are a high risk group for solid and hematologic malignancies. The risk seems to be influenced by age, chronic graft versus host disease and immunosuppressive drug regimens. Reports of oral malignant transformation in Fanconi Anemia after hematopoietic stem cell transplantation (HSCT) are increasing probably because of longer survival rates. This is the report of an 18- and her 28-year old sister who developed a post-HSCT oral squamous cell carcinoma. There were significant differences regarding time to malignant transformation, marrow donor characteristics and graft versus host disease evolution and treatment. The report reinforce the need for a routine head and neck screening for cancer in this particular syndrome and suggest that familial history should also be considered in Fanconi anemia patients at risk for oral malignancy after HSCT.