The role of bacteria in gallstone formation could not be conclusively evaluated until bacterial presence or absence in a stone was consistently shown. Cultural bacteriologic investigations at the time of cholecystectomy, however, led to the assumption that cholesterol gallstones were free of bacteria. In this study, we used a culture independent, molecular genetic approach to detect, quantify, and identify bacteria in cholesterol gallstones from 100 patients at the time of cholecystectomy and 6 months following. Bacterial growth was recorded in the culture in 9 of 100 gallstones; bacterial DNA, however, was detected in 82 of 91 sterile gallstones. High concentrations corresponding to between 10 6 to 10 7 bacteria/g were detected in 11 stones and low concentrations of 10 5 bacteria/g were detected in 71 sterile stones. The infection in stones with a positive bacterial culture was characterized by the predominance of single bacterial sequence(s) of the bacteria cultured. A similar predominance, indicating a recent infection, was found in sterile gallstones with low DNA concentrations. A high diversity of non-repeating bacterial sequences, possibly arising from previous overlapping infections, was found in sterile gallstones with high concentrations of bacterial DNA. After 6 months concentrations of bacterial DNA fell significantly in all groups of gallstones. As bacterial DNA is quickly destroyed upon storage, but is nevertheless readily found in most gallstones at the time of cholecystectomy, there must be a mechanism by which it is replenished. One such mechanism is the frequently reoccurring, possibly self-terminating infection and another one is the permanent colonization of the gallstone with bacteria at low concentrations. Both can promote cholecystolithiasis. (HEPATOLOGY 1998;27:662-665.)Our knowledge about the cholesterol gallstone comes primarily from the investigation of its composition at the time of cholecystectomy and from brief model experiments with saturated bile. Gallstone formation, however, takes years, and the vast majority of events that occur in the time between cholesterol crystal nucleation and their consolidation into a gallstone is not accessible to a direct investigation. Gallstone formation is, therefore, incompletely understood. Because cholesterol gallstones are more than 70% cholesterol and because bacteria are not regularly cultured at the time of cholecystectomy, the role of bacteria in the pathogenesis of cholesterol gallstones has been questioned. 1 Bacteria, however, are a good explanation for the initiation of nucleation. 2 Bacterial polymers are ideal substances for both binding loose cholesterol crystals to a massive gallstone and for building a matrix in which cholesterol later crystallizes. 3 Unfortunately, there is no convincing model to prove either of these hypotheses and the data about the occurrence of bacteria in bile, 4,6-7 the billiary tree, 5,8 and in the gallstones 8 are inconsistent.Bacteriologic findings depend on bacterial vitality and culturability. As bacteri...