A 30-year-old woman was admitted to our hospital because of recurrent ureterolithiasis. She was suspected of having adenine phosphoribosyltransferase (APRT) deficiency based on the presence of 2,8-dihydroxyadenine (DHA) crystals in her urinary sediment, infrared spectrophotometric analysis of the excreted stone, and then the definitive diagnosis by gene analysis. A pedigree study indicated only a slight possibility of this disease in the family. From these results, we consider that urinary sediment and stone analysis should be used for screening while gene analysis should be employed for definitive diagnosis of APRT deficiency, so that the complications of this condition can be prevented.