Evidence from recent studies has shown that the use of probiotics helps in the prevention and treatment of intestinal and extra-intestinal origin diseases, including liver and gallbladder disease. Gallstones (GS) are very common worldwide, affecting 10%–20% of the global adult population. GS is also considered a significant risk factor for gallbladder cancer (GBC). Approximately, 80% of GBC occur due to GS. Increasing evidence indicates that the gut-liver axis plays an important role in the pathophysiology of GS disease. Specific gut microbiota is found to be correlated with vulnerability to GS disease. Increased secretion of cholesterol by hepatic cells due to genetic, environmental, and dietary factors leads to formation of cholesterol GS. Moreover, reduced concentration of bile acid in bile increases the hyper saturation of bile with cholesterol which may lead to the formation of GS. Probiotics efficiently alter the composition of gut microbiota and bile acid synthesis, leading to health benefits such as lowering cholesterol, which is subsequently helpful in ameliorating hypercholesterolemia. With the multiple benefits of probiotics, this chapter aims to discuss the association of alterations in gut and biliary microbiota with GS formation and the influence of probiotics in the prevention and treatment of gallstone disease.