The peptidyl prolyl cis/trans isomerase Pin1, the human ortholog of yeast Ess1 specifically isomerizes peptide bindings of pSer/pThr-Pro residues in various proteins, and regulates the expression levels and functions of phosphorylated proteins. Activation of Pin1 is associated with pathology of a variety of diseases, such as cancer, Alzheimer's disease, infectious diseases and so on. Therefore, regulatory compounds for Pin1 can be applied as a clinical medicine against these diseases. Many chemists have exerted themselves to synthesize the inhibitors based on the 3D structure of Pin1. We have screened for the inhibitors against Pin1 from the natural products including the functional foods. Here we review the Pin1-associated pathology and the known inhibitors identified from natural products. And we introduce the screening methods targeting Pin1 activity.