The present study was confronted to exemplify the effect of α-Linolenic acid (ALA) (18:3, ω-3) and Linoleic acid (LA) (18:2, ω-6) on experimental intestinal toxicity induced by methotrexate (MTX). The groups of albino rats received, Group I: normal saline (2 ml/kg, i.p. sham control), Group-II : MTX (2.5 mg/kg, i.p. toxic control); Group-III: ALA (2 ml/kg, i.p.); Group-IV: LA (18:2, ω-6) (2 ml/kg, i.p.), Group-V : ALA (2 ml/kg, i.p.) andGroup-VI: LA (2 ml/kg, i.p.) with MTX (2.5 mg/kg, i.p.). Animals were sacrificed after 7 days treatment schedule and appraised for intestinal pH, total acidity, free acidity and colonic mucosal disease index (CMDI). Intestinal tissues were further evaluated for oxidative stress parameters (TBARS, SOD, protein carbonyl and catalase), and morphological modulation using scanning electron microscopy. The intestinal tissues were further graded for the enzymatic activities of COX-1, COX-2 and 15-LOX. Both ALA and LA demonstrated momentous protection against MTX induced intestinal toxicity, which could be attributed to their prooxidant nature.