Organophosphate pesticides are widely used in agriculture and household for pest control and consequently have been a major cause of toxicity in farmers and others especially in India. The present study was carried out to evaluate the ability of two pesticides: monocrotophos (MCP) and quinalphos (QNP) to generate oxidative stress and to explore the possible protective effects of melatonin in combating the caused stress. The purpose of the study was to find a suitable agent which could reduce the toxic symptoms generated due to acute as well as chronic exposure of monocrotophos and quinalphos. We studied the potential of MCP and QNP to generate oxidative stress and subsequent oxidative damage to DNA in the rat tissues and lymphocytes. Oxidative stress was measured by quantitating the levels of reactive oxygen species (ROS), total antioxidant capacity, accumulation of lipid peroxidation end products while DNA oxidation was measured by the modified comet assay using the bacterial repair enzymes, formamidopyrimidine glycosylase (Fpg) and endonuclease III (Endo III) in the liver, brain and lymphocytes of rats given for two days and subchronic exposure of MCP and QNP, both separately and in combination. The results showed that both acute and subchronic pesticide exposure, separately and in combination, lead to the generation of oxidative stress. Extensive oxidative damage of both purine and pyrimidine bases was observed in liver, brain and lymphocytes of rats given exposure with MCP or QNP, separately or in combination. MCP was found to be more toxic than QNP as highest DNA damage was observed in this group of rats. The combined exposure of MCP and QNP does not potentiate each other's action. However, co-treatment of melatonin, a well established antioxidant, decreased the oxidative stress and damage caused to the DNA.