Type 1 glycogen storage disease is caused by glucose-6-phosphatase deficiency and nephrolithiasis is the most common renal complication. Although urate stones are the most common stone type, metabolic alterations favoring calcium nephrolithiasis has also been described in these patients. We report a pediatric case with type 1 glycogen storage disease presenting with recurrent macroscopic hematuria that was diagnosed to have calcium stone disease. The patient had multiple metabolic abnormalities including hypercalciuria, hyperoxaluria, hypocitraturia and hypomagnesuria.