Diagnosis of chronic pancreatitis in its early stage is an extremely difficult task. If the genetic predispositions are identified, it may help make possible the earlier diagnosis of chronic pancreatitis or the detection of patients at risk. There are two major hypotheses about the pathogenesis of chronic pancreatitis known as the "necrosis-fibrosis" and "pancreatic stone protein" hypotheses. Recent molecular and genetic evidence suggests that both pathways contribute to the pathogenesis of chronic pancreatitis. Chronic pancreatitis may be caused by either increased proteolytic activity [the cationic trypsinogen (PRSS1) gene] or decreased protease inhibition (the pancreatic secretory trypsin inhibitor (PSTI) gene]. The impaired pancreatic duct function [cystic fibrosis transmembrane conductance regulator (CFTR) gene] may also be involved in the pathogenesis of the disease. Except for PRSS1 mutations, the known genetic risk for chronic pancreatitis is not high. The high individual variability and low incidence of chronic pancreatitis suggest that yet unidentified genetic and environmental factors are important. Further genetic analysis is necessary for understanding the pathogenesis of chronic pancreatitis, which may be helpful for the earlier diagnosis of the juvenile- or young-onset disease.