Intestinal ischemia/reperfusion (I/R) injury is known to result from both tissue hypoxia and the consequences of reperfusion of ischemic tissues. In addition, ATP stores are depleted during ischemia because of the relatively inefficient production of ATP by glycolysis. In this study, the effect of melatonin on some important metabolic enzymes hexokinase (HK), glucose-6-phosphate dehydrogenase (G6PD), lactate dehydrogenase (LDH) and malate dehydrogenase (MDH) responsible for generation of energy was investigated. Melatonin was determined to cause a distinct regulation of these enzymes. While the activity of the enzyme HK of the first step of glycolysis was significantly higher in pre-melatonin treated I/R group than group I/R animals, the activities of LDH and G6PD were decreased markedly with melatonin application. Although, the MDH levels of pre-melatonin treated I/R group were higher than the sham control group, this might not be a result of melatonin application, since both I/R and I/(Mel/R) groups also showed even higher MDH activity than the control group.