Lignocellulosic biomass, rich in hexose and pentose sugars, is an attractive resource for commercially viable bioethanol production. Saccharomyces cerevisiae efficiently ferments hexoses but is naturally unable to utilize pentoses. Metabolic engineering of this yeast has resulted in strains capable of xylose utilization. However, even the best recombinant S. cerevisiae strains of today metabolize xylose with a low rate compared to glucose. This study compares the transcript profiles of an S. cerevisiae strain engineered to utilize xylose via the xylose reductase-xylitol dehydrogenase pathway in aerobic chemostat cultures with glucose or xylose as the main carbon source. Compared to the glucose culture, 125 genes were upregulated, whereas 100 genes were downregulated in the xylose culture. A number of genes encoding enzymes capable of nicotinamide adenine dinucleotide phosphate regeneration were up regulated in the xylose culture. Furthermore, xylose provoked increased activities of the pathways of acetyl-CoA synthesis and sterol biosynthesis. Notably, our results suggest that cells metabolizing xylose are not in a completely repressed or in a derepressed state either, indicating that xylcose was recognized neither as a fermentable nor as a respirative carbon source. In addition, a considerable number of the changes observed in the gene expression between glucose and xylose samples were closely related to the starvation response.