1 Calcium stones. 2  Most kidney stones are calcium stones, usually in the form of calcium oxalate. 3  Oxalate is a naturally occurring substance found in food. 4  Some fruits and vegetables, as well as nuts and chocolate, have high oxalate levels. Certain genetic factors also may increase your risk of uric acid stones. 2  Cystine stones. 3  These stones form in people with a hereditary disorder that causes the kidneys to excrete too much of certain amino acids (cystinuria). 4  Other stones. 5  Other, rarer types of kidney stones also can occur.