Background: Malathion (MAL) is the most organophosphates which is capable to produce free radicals and induce disturbance in body antioxidant. This study was undertaken to assess the effects of Kefir (KF), a probiotic fermented milk, on oxidative stress, functional and metabolic, as well as histological damage induced by malathion to the kidneys and liver of rats. Materials and Methods: Thirty‑two Wistar rats were divided randomly into four groups (n = 8): sham (saline/corn oil), KF group (1.8 ml/day); MAL control treated groups (50 mg/kg); and KF/MAL‑treated group. Treatments were administered for 30 days through oral gavage. Twenty-four hours after the last treatment, Parameters related to the function and the histology of both kidneys and liver were evaluated and statistically analyzed from kidney, liver and blood serum samples in respect of the groups. Results: Malathion increased the levels of various serum marker enzymes aspartate aminotransferase (AST), alanine aminotransferase (ALT) and Alkaline phosphatase (ALP) and it increased bilirubin concentration. MAL also increased serum urea, uric acid and creatinine, whereas it decreased albumin level. As well as MAL induced increase in MDA in both liver and kidneys tissues while induced decreases in the activities of SOD and CAT and GSH activity. Co-administration of KF with MAL resulted in improvement of all tested parameter. In histological study of liver and kidney, MAL induced damage in liver and kidneys tissues. However, KF administration to MAL-intoxicated animals resulted in overall improvement in liver and kidneys tissue damage, emphasizing its antioxidant role. Conclusion: In light of the available data, it can deduce that MAL-induced lipid peroxidation, oxidative stress, liver and kidneys damage in rats, and conjoint supplementation of KF has resulted in pronounced ameliorating effect in all tested parameter and histological picture of liver and kidney tissues.