This research work examins the cost structure of food industries of Pakistan. The purpose the research is to identify the most suitable functional form for the KLEM model for food industries of Pakistan. The elasticities of substitution, own-price and cross-price elasticities, and cost elasticity of output are estimated using cross section data from Census of Manufacturing Industries of Pakistan 2005-06. Christensen, Jorgensen and Lau developed transcendental logarithmic cost function; a more flexible functional form is applied in the research paper. We estimated the trans-log cost function using iterative Zellner’s methodology. Allen’s partial elasticities of substitution show strong substitution between labor and capital. Capital and energy are good substitutes but material is not a close substitute for capital and energy. Own price elasticities indicate that material is least responsive to a change in its own price while other rest of the inputs are more price-elastic. The output elasticity of cost demonstrates the presence of economies of scale.