Kidney matrix stones are a rare form of calculi, which are challenging to diagnose. Matrix stones consist of a proteinaceous material which has a radiolucent appearance that might be overlooked on imaging. Recently, endourological intervention has been the standard treatment method for matrix stones. We report a case of urinary matrix stones in a patient with type 1 diabetes mellitus and chronic kidney disease, in whom the stones formed into a pure matrix and were not visualized in the computed tomography scan. The stones were found after additional work-up, and they were managed using a transureteral stone basket, not through endourological intervention.