The extensive use of malathion, an organophosphate pesticide, raises the possibility of its undesirable toxicity to non-target organisms. Agricultural run-off and vector control sprays are the major sources of exposure to this pesticide for aquatic organisms. Some earlier studies have reported the presence of malathion at concentrations ranging from 18.12μg/L to 105.2μg/L in various water samples. In this study, we have tested the hypothesis that these sub-lethal yet environmentally significant concentrations of malathion has serious toxicological implications on the fingerlings of Labeo rohita. Exposure to increasing concentration of malathion (10, 50 and 100μg/L) was reflected in the serum concentration of the pesticide and also in the inhibition of acetylcholinesterase activity in fish brains. Increased abnormalities in liver function test coupled with a rise in the oxidative stress response were observed in gills, liver and kidney. However, the increase in antioxidant enzyme activities like superoxide dismutase and glutathione-S-transferase by malathion exposure suggested a hormetic response. Tissue injury due to malathion was evident from the morphological and nuclear anomalies in the H-E stained sections of gill, liver and kidney. Cell cycle analysis of these organs further fortified the histopathological findings. This study elucidates the sub-lethal toxicity of environmentally relevant malathion concentrations on Labeo rohita which indicates the potential health hazard posed to human beings consuming this fish. This calls for careful application of malathion in areas adjoining to inland fisheries.