Plasma from 126 patients with various autoimmune diseases and 118 healthy subjects were examined to determine the presence of autoantibodies to FKBP12, one of immunophilins. The frequency of IgG and/or IgM anti-FKBP12 autoantibodies detected by ELISA was as follows; SLE (15/39), SSc (11/27), CREST (4/7), RA (2/8), MCTD (0/5), Graves' disease (4/12), IDDM (2/6), PM/DM (0/3), MG (1/4), AIH (2/6), PBC (4/9), and healthy subjects (5/118). The specificity of the autoantibodies was demonstrated by absorption of the plasma samples with r-FKBP12 and other recombinant proteins. In immunoblotting, IgM anti-FKBP12 autoantibodies reacted with two bands of 12 and 24 kD, the latter representing the dimer. Anti-FKBP12 autoantibodies in some patients reacted more strongly with the dimer than the monomer, suggesting that FKBP12 may also exist as the dimer in vivo. The majority of anti-FKBP12 autoantibodies bound to two synthetic peptides corresponding to amino acid residues of FKBP12, Pro16 approximate to Tyr26 and Thr27 approximate to Phe46. These epitopes are phylogenetically well conserved and responsible for the binding to calcineurin and FK506. The autoantibodies inhibited pentamerization of FKBP12 with FK506, calcineurin, calmodulin, and Ca2+ in vitro. These data define the frequent occurrence of a novel set of autoantibodies to a cytosolic protein involved in the regulation of the immune response.