Widely used malathion (MLT) causes environmental pollution, leading to toxicity in many living things, including humans. Rutin (RUT) is a flavonoid with various biological properties. In the present study, the protective effects of rutin against liver and kidney toxicity caused by malathion were investigated. In the study, MLT (100 mg/ kg) and RUT (50 or 100 mg/kg) were administered to rats alone or in combination for 28 days. Then, oxidative stress, inflammation, endoplasmic reticulum stress (ERS), apoptosis, and autophagy markers in liver and kidney tissues were analyzed by biochemical and molecular methods. The results showed that MLT caused oxidative stress in both tissues, while RUT showed antioxidant properties and protected these tissues from oxidative damage. Moreover, MLT upregulated the expressions of ATF-6, PERK, IRE1, GRP78, and CHOP, leading to ERS. However, RUT alleviated ER stress and suppressed these markers. The study also found that MLT increased inflammatory, apoptotic, and autophagic markers. All these factors affected liver and kidney functions and caused an increase in plasma ALT, AST, urea, and creatinine levels. On the other hand, it has been observed that RUT may protect liver and kidney tissues from the destructive effect of MLT by showing anti-inflammatory, antiapoptotic, and anti-autophagic properties. Thus, it was determined that ALT, AST, urea, and creatinine levels decreased after RUT treatment. As a result, it was observed that MLT had a toxic effect on the liver and kidney tissues of rats, and it was determined that this toxicity could be alleviated by RUT treatment.