Disclosed are methods, compositions and formulations for treating or preventing hypercalciuria thereby reducing the risk of nephrolithiasis and normalizing urine chemistry and composition. The method includes administering vitamin K2 in a medicinal or nutritional composition, preferably without calcium, optionally in combination with a therapeutic dose of one or more selected from the group consisting of: a citrate salt, magnesium oxide, a bicarbonate salt and vitamin B6.