Peptidyl prolyl cis/trans isomerases (PPIases) are the enzymes that increase the rate of isomerization of the peptide bond N-terminal to the proline substrate. Parvulin14 (Par14) and its isoform Par17 belong to the Parvulin family which is the third family of PPIases. Par14 was shown to bind the DNA. Par14 was also proposed to be a part from the pre-ribosomal ribonucleoprotien complexes and an RNA processing factor that is involved in ribosome biogenesis. The longer isoform Par17 was shown to be expressed only in the Hominidae, and is targeted to the mitochondria. In order to find binding partners for Par14/17 (peptides or proteins), we applied the high through-put screening methods, the yeast two-hybrid (Y2H) and the phage display (Ph.D.). In our Y2H study we show a target-unrelated protein that may confuse a number of Y2H results. In our Ph.D. screening against PinA of Cenarchaeum symbiosum we selected a peptide that binds PinA with low affinity; however we used this peptide to map PinA putative PPIase active site, and to show a flexible region of PinA. The flexibility of this region is probably a general feature of the peptidyl prolyl cis/trans isomerization. Furthermore, we panned 7 and 12-mer peptide libraries against Par17. One consensus sequence was enriched from both libraries, XHSXVHØ, where X can be any amino acid and Ø is a hydrophobic amino acid. We demonstrate the binding of this motif to Par14/17 with phage ELISA and NMR spectroscopy where we could show that this motif is binding to the PPIase domain of Par14/17. Moreover, using these peptides we map the PPIase active site of Par14/17. Our peptides can be used to design peptides to study the PPIase activity of Par14/17, and to elucidate the motif that Par14/17 recognizes in vivo.