Recent reports suggest that bone marrow might serve as a source of skin progenitor cells. Graft-versus-host disease (GVHD) is a systemic disease that involves the skin, the liver, and the gastrointestinal tract, and contributes to transplant-related morbidity and mortality. To evaluate whether donor-derived bone marrow cells participated in its pathophysiology, we correlated the severity of GVHD in skin from sex-mismatched recipients with the percentage of donor-derived keratinocytes using fluorescence in situ hybridization (FISH) for detecting the Y chromosome. Y-positive signals were observed in female epidermis in both keratinocytes and lymphocytes. These results support the notion that donor-derived hematopoietic stem cells may contain pluripotent stem cells. Furthermore, there was a strong correlation between the frequency of Y-positive keratinocytes and the histopathologic grade of GVHD (p = 0.004), as well as with the number of Y-positive lymphocytes infiltrating the epidermis (p = 0.005), suggesting a role for donor-derived keratinocytes in the pathophysiology of GVHD. However, no clusters of Y-positive keratinocytes were found in the epidermis, and no correlation was observed between the number of Y-positive keratinocytes and time course of GVHD after transplantation. We hypothesize that donor-derived stem cells may play a role in the regeneration of damaged keratinocytes in GVHD.