A 16-month-old girl diagnosed with osteopetrosis underwent an unrelated, partially matched (with major mismatch at A locus) cord blood stem cell transplant. Twelve months later she developed severe acute autoimmune hemolytic anemia (AIHA). Immunophenotype analysis of lymphocyte subsets 8 months post transplant showed a low number of T lymphocytes, with normal subsets, and with NK cells and B lymphocytes within normal ranges. When the hemolytic anemia developed, the lymphocytes subsets changed and analysis showed higher numbers of B lymphocytes than previously, lower CD3+ T lymphocytes with inversion of the CD4/CD8 ratio and an abnormal proportion of T lymphocyte subsets. She was being treated with cyclosporine, and steroids and immunoglobulins were added. Initially the AIHA improved, but repeated infectious episodes led us to tail off the immunosuppressive treatment. The AIHA relapsed and cyclosporine was restarted. Currently, she is on cyclosporine and low-dose steroid treatment with no hemolytic features. During the 3 months when the AIHA was being treated, she developed extensive skin cGVHD and recurrent pneumothoraces. AIHA may be the first manifestation of abnormal reconstitution of immunity developing after a hematopoietic transplant. This abnormal reconstitution is also the basis of cGVHD. We suggest that aggressive immunosuppressive treatment with intensive measures against infection could give a better prognosis to such patients.