Intrahepatic stone is prevalent in Asian countries; though the incidence declines in recent years, the number of patients is still in a large quantity. Because of multiple complications, high recurrence rates, serious systemic damage, and a lack of extremely effective procedure for the management, it is more important to find out the etiology and pathogenesis of intrahepatic stones to prevent the disease from happening and developing rather than curing. A number of factors contribute to the development of the disease, such as cholestasis, infection, and anatomic abnormity of bile duct and bile metabolic defect. The four factors and possible pathogenesis will be discussed in detail in the review.