Due to environmental and economical concerns, there is a high demand for a renewable fuel source. Bio-ethanol from lignocellulosic biomass is one such renewable fuel. Before this can be realized many problems need to be addressed. One major problem is the existence of multiple inhibitors found in a typical lignocellulosic hydrolysate. The more predominant inhibitors include furfural, hydroxymethylfurfural (HMF), and vanillin. These chemicals inhibit growth and fermentation of the yeast, Saccharomyces cerevisiae. In attempt to understand the genes involved in inhibitor tolerance we performed a screen looking for yeast mutants that exhibited altered growth in the presence of HMF. Genes isolated from this screen included those involved in telomere maintenance, protein and ergosterol metabolism, the pentose phosphate pathway, mitochondria and vacuole function, gene transcription, generalized stress tolerance, and genes of unknown function. Interestingly, there were many similar genes and pathways found in the HMF screen compared to the screen for furfural and vanillin tolerance. This suggests that similar pathways exist in yeast for protection against multiple inhibitors found in a lignocellulosic hydrolysate. To further investigate these similarities we analyzed some of these common genes with a focus on genes involved in the pentose phosphate pathway, ergosterol biosynthesis, telomere maintenance, and oxidative stress protection. Yeast cultures with one of these genes mutated, overexpressed, or exogenous gene product added were examined for their ability to grow in the presence of HMF, furfural, or vanillin. In addition, under these same conditions, yeast cell physiology and the accumulation of reactive oxygen species were quantified.