A large body of physiological, cell biological, kinetic and structural data about peptidyl prolyl cis/trans isomerases (PPIases) has been accumulated during the past 20 years, but despite the simplicity of the catalyzed reaction the question of how the enzyme action is performed is still not fully answered. In this review the center of attention is the molecular background of the catalytic mechanism of PPIases and the spontaneously occurring peptidyl prolyl cis/trans isomerization. We summarize and compare the available kinetic, structural and amino acid sequence data of all three PPIase families, the cyclophilins, FKBP and parvulins. Different catalytic mechanisms that have been suggested in the literature are discussed. A comprehensive comparison of enzyme active site structures reveals a hitherto unnoticed similarity between the three PPIase families and might suggest that PPIases utilize mechanisms that are more similar than previously suspected.