One way to optimize methane production in anaerobic digestion plants is to substitute ligno-cellulosic by-products for crops traditionally used as energy sources. However, using these by-products requires introduction of a pre-treatment system to minimize energy input and maximize energy output for an improved net energy equation. In this study, four agricultural byproducts (wheat, barley, rice straw and maize stalks) underwent various mechanical and thermal treatments prior to anaerobic digestion including particle size reduction to 5.0, 2.0, 0.5, and 0.2 cm and heat application to 90 degrees C and 120 degrees C. Mechanical pre-treatment increased byproduct methane yields more than 80%; thermal pre-treatment improved yields more than 60% for wheat and barley straw. Pre-treating wheat straw improved methane yields most, regardless of whether the method was thermal or mechanical. An electric net energy balance was also completed to analyze the feasibility of the pre-treatments according to input and output of energy. (C) 2011 Elsevier Ltd. All rights reserved.