Foxtail millet (Setaria italica), consumed by the rural and tribal populations in South India, is a rich source of nutrients. Fermentation by endogenous microflora increased the total soluble sugars and reducing sugars with a simultaneous decrease in the starch content. The protein extractability and albumin/globulin fractions were improved. The beneficial long-chain fatty acid profile of raw flour was retained. Acetic and butyric acid were the major short-chain fatty acids produced. Most of these changes occurred in the first 24 h of fermentation.