This article addresses development of the Illinois ethanol industry through the period 2007-2022, responding to the ethanol production mandates of the Renewable Fuel Standard by the U.S. Environmental Protection Agency. The planning for corn-based and cellulosic ethanol production requires integrated decisions on transportation, plant location, and capacity. The objective is to minimize the total system costs for transportation and processing of biomass, transportation of ethanol from refineries to the blending terminals and demand destinations, capital investment in refineries, and by-product credits. A multi-year transshipment and facility location model is presented to determine the optimal size and time to build each plant in the system, the amount of raw material processed by individual plants, and the distribution of bioenergy crops and ethanol.