The occurrence of autoantibodies and their relation to chronic graft-versus-host disease (GVHD) have been studied in children, 100 days or more following allogenic bone marrow transplantation (BMT), mainly performed for a variety of genetic disorder. Seventeen of 40 patients had autoantibodies to thyroid microsomes, compared with none of 46 control children of similar age (p less than 0.001). The presence of these antibodies was strongly associated with chronic GVHD (14 of 20 patients), p = 0.001. IgG antibodies to the cytoplasm of squamous epithelial cells were demonstrated in 15 of 36 children following transplantation (p less than 0.001), none being found in 46 normal children. The incidence and titre of these antibodies were significantly higher in patients with chronic GVHD (p = 0.041 and p = 0.019 respectively). Despite there being a significant number of patients with antibodies to nuclei, smooth muscle and gastric parietal cells, these autoantibodies were not related to the presence of chronic GVHD. Although the mechanism of production is not known, antibodies to thyroid antigens and the cytoplasm of squamous epithelial cells may be useful markers for GVHD.