Lignocellulosic biomass is a source of low cost polysaccharides that some microbes can deconstruct and convert into liquid transportation fuel. Feedstocks vary in their ease of use depending on their source and handing. Estimating conversion amenability is useful to determine the effects of biomass pretreatment and genetic potential for the purposes of energy crop breeding and genetics. Here we describe a small-scale high-throughput assay that measures ethanol production from a culture of plant biomass and the ethanologen Clostridium phytofermentans.