Immobilization is an effective method to increase ethanol production, as proven by previous research. Results almost exclusively demonstrate an increase in ethanol production by and decrease in reproduction rate of immobilized Saccharomyces cerevisiae cells. Recently, research has been conducted to determine the cause of this change. The extreme variance in results due to lack of technology makes it difficult to determine the cellular changes induced by immobilization. With the advent of new technology, specifically gene expression analysis, the RNA content of cells can be easily and rapidly analyzed. S. cerevisiae cells were immobilized in 3% (w/v) calcium alginate beads and grown inside of a packed bed reactor for comparison to planktonic cells growing in batch and chemostat cultures. Temperature inside of the reactor was maintained at 33 C with a pH of 5.5. Cell concentration inside of the beads was monitored periodically in order to create growth curves. Bud scar numbers of immobilized cells were also counted and compared to suspended cells. Scanning electron microscopy images of the alginate beads were taken to determine cell growth inside of the beads. Affymetrix Yeast 2.0 gene chips were used, and the data retrieved was analyzed with GeneSpring software using the Bioconductor packages. Results indicated changes in expression of 3,559 genes with significant difference among treatments by a factor of 2-fold or greater. One-way ANOVA of the filtered data yielded 380 highly significantly different genes between immobilized and suspended cells. Many of the genes pertaining to glycolysis exhibited increased expression levels. Several genes necessary for reproduction were expressed at lower levels in the immobilized cells than in their planktonic counterparts. Many different gene ontologies are discussed, and the expressed genes are mapped onto biochemical pathways.