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The changes in chemical composition, antioxidant activity and fatty acid composition of lentil flour after dehulling, germination and cooking of seeds were investigated. Dehulling showed no significant effect on protein content, however, protein content decreased in most of the varieties after germination and cooking. Total soluble sugars (TSS) content increased significantly after dehulling (2.0-41.64 %) and cooking (2.08-31.07 %) whereas, germination had no significant effect on TSS content. Total lipids increased significantly after dehulling (21.56-42.86 %) whereas, it decreased significantly after germination (2.97-26.52 %) and cooking (23.05-58.63 %). Cooking was more effective than other methods in reducing trypsin inhibitors (80.51-85.41 %). Dehulling was most effective in reducing tannins (89.46-92.99 %) and phytic acid (52.63-60.00 %) content over raw seed. Myristic, palmitic, stearic, oleic and linoleic acid content decreased while linolenic acid content increased after dehulling. Dehulling, germination and cooking decreased the content of antioxidant metabolite (gallic acid, catechin and quercetin) and also antioxidant activities. Raw samples followed by germinated samples showed the highest concentrations of phytochemicals responsible for antioxidant activity and also the antioxidant capacities. Present study showed germination and cooking would be useful in formulation and development of lentil based functional foods for human health benefits.