A new inhibitor for peptidylprolyl cis-trans isomerase (PPIase) has been isolated from Ganoderma lucidum and purified to homogeneous state by organic solvent extraction. The purified PPIase inhibitor (GPI) is assumed to be a membrane-associated glycoprotein. GPI inhibits specifically the bovine brain PPIase, a cyclophilin, and has no effect on the FKBP activity. The results of our chemical modification study of GPI indicate the presence of Lys residue(s) at or near its binding site. Like CsA-cyclophilin complex, GPI-bovine brain PPIase complex strongly inhibits the calcineurin activity in vitro, suggesting the possible involvement of GPI in immunomodulating pathway by the formation of PPIase-inhibitor-calcineurin complex.