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Nonalcoholic fatty liver disease (NAFLD) is known to be a health-related problem; there is no proven treatment for NAFLD. However, a wide range of possible therapies have been proposed and studied. In the current study, we aimed to compare the therapeutic effects of fenofibrate and pioglitazone on NAFLD.In this randomized clinical trial study (ethic number: ZUMS.REC.1393.133), patients with NAFLD and alanine aminotransferase in range of 1–1.5 folds of normal and BMI (25–35) were studied. Blood lipids and liver enzymes were measured. The patients were divided randomly into three groups (recipient of fenofibrate, pioglitazone, and exercise). After the patients completed the course of treatment, liver enzymes were measured.According to the results of this study, 90 patients with NAFLD were divided into three groups of 30 patients. All variables at the beginning of the study showed no significant difference among the three groups, but after the treatment period, the results showed that the levels of alanine aminotransferase, aspartate transaminase, systolic blood pressure, diastolic blood pressure, and BMI changed significantly: the levels decreased in all groups.This study showed beneficial effects of fenofibrate and pioglitazone in patients with fatty liver. Further studies with larger study populations on the effects of these drugs on fatty liver, lipid profile, blood glucose, and insulin are suggested.