Aspiration is a devastating complication during decontamination procedure in poisoning patients. We have investigated whether S-methylisothiourea protects different pulmonary aspiration gastrointestinal decontamination agent-induced lung injury in rats. Forty-two male Sprague-Dawley rats were assigned to one of six groups (n = 7): normal saline, activated charcoal, polyethylene glycol, normal saline + S-methylisothiourea treated activated charcoal + S-methylisothiourea treated and polyethylene glycol + S-methylisothiourea treated. Normal saline, activated aharcoal and polyethylene glycol were instilled into the lungs. The rats received S-methylisothiourea i.p twice daily for 7 days. Serum surfactant protein D, oxidative stress products and inducible nitric oxide synthase expression in the lung were investigated. The aspiration of activated charcoal significantly increased all histopathological scores (P < 0.01). Only peribronchial inflammatory cell infiltration, alveolar edema, and alveolar histiocytes were increased in the polyethylene glycol groups as compared to the normal saline group (P < 0.05). Pulmonary aspiration increased serum malondialdehyde (P < 0.001), and surfactant protein D (P < 0.05) levels and decreased serum superoxide dismutase levels (P < 0.05). S-methylisothiourea treatment decreased all histopathological scores in the activated charcoal treated S-methylisothiourea group (P < 0.01) and only decreased alveolar edema and alveolar histiocytes in the polyethylene glycol-treated S-methylisothiourea group (P < 0.05). S-methylisothiourea treatment reduced elevated oxidative factors, inducible nitric oxide synthase activity and serum surfactant protein D levels. Our findings showed that S-methylisothiourea may be a protective drug against Activated Charcoal and Polyethylene Glycol-induced lung injury.