This investigation has been conducted to study the protective effect of Thymoquinone against Streptozotocin induced diabetes in rats. The rats were allocated into four groups each group contain seven animals; Control, Thymoquinone, Streptozotocin, Streptozotocin + thymoquinone. Control group was injecteda single dose by intra-peritoneal injection of saline (0.5ml/kg), Thymoquinone group provided thymoquinone (4mg/kg) with drinking water, Streptozotocin group was injecteda single doseby intra-peritoneal of streptozotocin (40 mg/kg) and thymoquinone was provided (4mg/kg) with drinking water three days after streptozotocin was injected a single dose intra-peritoneal injection of streptozotocin (40 mg/kg)to the streptozotocin+ thymoquinone group. Three days after the administration of streptozotocin, the development of diabetes in two experimental groups was confirmed by measuring the glucose levels in the blood. Eight days after the beginning of the experiment the rats were anesthetized then right kidney was taken for process was followed for light microscopic research. The kidney volume and glomerular number were calculated for each group using physical disector. A significant increase of the kidney volume in streptozotocin group andstreptozotocin + thymoquinone. A significant decreased glomerular number in streptozotocin group.