The risk of late complications including secondary malignancies is increased in long-term survivors of allogeneic hematopoietic stem cell transplants (HSCT). There is limited literature on the biological behavior and clinical features of squamous cell carcinoma (SCC) of head and neck post-HSCT. We present the clinical and pathologic characteristics on six patients who were diagnosed with SCC while in remission following an allogeneic HSCT. Median follow-up was 8 years. Five patients (83%) developed SCC of tongue and one developed esophageal SCC. Five patients had oral chronic graft-versus-host disease (cGvHD). The conventional risk factors of alcohol, tobacco, and human papillomavirus were absent. The most common presenting finding was the new-onset focal oral pain and ulcerated plaques clinically indistinguishable from a flare of their oral cGvHD lesions. We demonstrated that the SCC in three patients was of donor origin.