We report on a case of unilateral and diffuse xanthogranulomatous pyelonephritis (XGP) associated with Crohn’s disease and primary hyperparathyroidism (HPT). The patient had undiagnosed primary HPT for at least a year prior to presentation. The co-existence of Crohn’s disease and primary HPT caused calcium oxalate stone likely by the known mechanism of hypercalcemia and hyperoxaluria respectively. The patient developed XGP, a rare disease, as a result of infected calcium oxalate stone which was treated with antibiotics and unilateral nephrectomy. To the best of our knowledge, this is the first case of XGP associated with Crohn’s disease and primary HPT.