Phosphorylation of proteins on serine or threonine residues preceding proline is a pivotal signaling mechanism regulating cell proliferation. The recent identification and characterization of the enzyme peptidyl–prolyl cis/trans isomerase never in mitosis A (NIMA)-interacting 1 (PIN1) has led to the discovery of a new mechanism regulating phosphorylation in cell signaling. PIN1 specifically binds phosphorylated serine or threonine residues immediately preceding proline (pSer/Thr-Pro) and then regulates protein functions, including catalytic activity, phosphorylation status, protein interactions, subcellular location, and protein stability, by promoting cis/trans isomerization of the peptide bond. Recent results have indicated that such conformational changes following phosphorylation represent a novel signaling mechanism in the regulation of many cellular functions. Understanding this mechanism also provides new insight into the pathogenesis and treatment of human hepatocellular carcinoma. A better understanding of the role of PIN1 in the pathogenesis of hepatocellular carcinoma may lead to the identification of molecular targets for prevention and therapeutic intervention.