A diagnostic algorithm is proposed for diagnosis of complete APRT deficiency. Stone analysis (combining morphologic examination by stereomicroscope and infrared spectroscopy) allows identification of 2,8-DHA in virtually all cases. When observed by microscopy in urine samples or renal biopsy in patients with crystalline nephropathy, crystals should be studied by Fourier transformed infrared microscopy, which represents a highly specific and sensitive technique. In a second step, diagnosis of APRT deficiency must be confirmed by measure of APRT activity level in erythrocyte lysates. APRT activity assay may also be helpful in patients without analyzable stone, especially when crystalluria cannot be studied (e.g., patient with anuria; technique not available). Aprt gene analysis, although not necessary for diagnosis, may be performed to identify mutations.