FKBP36 has been previously shown to be a crucial factor in spermatogenesis. Loss of FKBP36 disrupts meioses in pachyten causing infertility in male rodents. FKBP36 belongs to the group of TPR-motif containing FKBPs known to be involved in assembly and regulation of multi-enzyme-complexes. In order to supplement the genetically and immunohistochemically investigations the FKBP36 protein was characterized extensively by biochemical methods. Several parts of the human FKBP36 cDNA were cloned into expression vectors. After expression, the corresponding proteins were purified and investigated. Existence of secondary structure elements was revealed by CD-spectroscopy. Although the protein shows homology to FKBP, it could be shown that the wildtype FKBP exhibits no PPIase activity in the established assays. By means of structural modeling a protein variant FKBP36 R811L was designed, showing characteristic PPIase activity. Additionally, Hsp90, Hsp72, Clathrin heavy chain and GAPDH have been identified as specific interaction partners of FKBP36 by a co-precipitation assay. Interaction sites were shown to be localized on different protein regions and interactions occur restricted within distinct subcellular compartments. FKBP36 participates in different multi-protein-complexes and may be multifunctional. By binding and inhibition of GAPDH it possibly regulates cellular metabolism and by interaction with HSP72 it belongs to the essential components of meiotic signal transduction.