Although, the effectiveness of allogeneic hematopoietic stem cell transplantation (HSCT) is, in large part, due to the destruction of recipient malignant cells by donor immune cells, the antigenic targets of this response in most patients are not well defined. In previous studies we demonstrated that patients with multiple myeloma (MM) who achieved a complete response after HSCT and donor lymphocyte infusion (DLI) developed high titer antibodies to a variety of antigens expressed by myeloma cells. Dihydrolipoamide acetyltransferase, the E2 component of the pyruvate dehydrogenase complex (PDC-E2) was one of the antigens identified in this screen. Importantly PDC-E2 is the immunodominant auto-antigen in primary biliary cirrhosis (PBC), a liver autoimmune disease in which greater than 95% of patients develop auto-antibodies against the inner lipoyl domain of this mitochondrial antigen. To further characterize the antibody response against PDC-E2 after allogeneic HSCT, we developed a sensitive ELISA to measure antibody responses to GST-PDC-E2 fusion protein. PDC-E2 antibodies following HSCT were compared to 52 normal donors and 50 patients with PBC. All samples were tested at 1:50 or 1:100 dilution. PDC-E2 antibodies were not detected in 20 patients with MM at the time of diagnosis, 10 patients with hematologic malignancies after allogeneic HSCT who did not receive DLI and 10 patients with chronic graft-versus-host disease (GVHD). However, when screening patients who achieved complete remission after DLI, PDC-E2 antibodies were detecting in 3 out of 10 patients with MM, 1 out of 5 patients with chronic myelocytic leukemia (CML) and 1 out of 2 patients with chronic lymphocytic leukemia (CLL). Although some of these patients developed GVHD, none developed chronic liver disease. In each case, PDC-E2 antibodies were only detectable after DLI and not pre-HSCT or pre-DLI. In 2 patients with particulary high titer antibodies (detectable down to 1:10,000 dilution) anti-PDC-E2 persisted for more than 2 years post-DLI and the dominant Ig subclasses at all time points were IgG1 and IgG2. The specificity of PDC-E2 antibodies post-DLI was also tested by ELISA against a panel of 85 overlapping peptides representing the entire amino acid sequence of PDC-E2 and by western blot against 2 common mitochondrial auto-antigens, branched-chain alpha-keto acid dehydrogenase (BCKD) and 2-oxoglutarate dehydrogenase (ODGC). Post-DLI sera were not reactive with BCKD or ODGC and most samples specifically recognized 2 peptides located in the E2 catalytic domain of PDC-E2. In contrast, serum from PBC patients had a different pattern of reactivity and were primarily directed against peptides in the inner lipoyl domain of PDC-E2. In conclusion, we demonstrate that patients with hematologic malignancies who achieve complete remission following DLI frequently develop allogeneic antibody responses directed against one of the most common auto-antigens in PBC. However, the epitope specificity of the antibody response following allogeneic HSCT is distinct and is not associated with chronic liver disease.