Gene expression analysis has become a standard tool for studies of biological models of disease processes, growth, and development and has been used increasingly in the field of clinical research. The completion of the human genome sequence is now providing the glycomics research community with the tools to develop a synergism with related fields such as MS glycan profiling and proteomics. The use of microarray technology to measure changes in gene expression is a useful approach for the study of the expression profiles of glycosyltransferases, carbohydrate binding proteins, and related enzymes. The availability of standardized microarray platforms, high-quality reagents for sample preparation and hybridization, and image and statistical analysis tools has contributed to recent advances in the application of this technology to glycobiology. Most microarray experiments today are done within specialized core facilities equipped with instrumentation, software, and personnel with expertise in their application. The focus of this chapter is on aspects of microarray analysis common to all platforms and within the realm of the glycobiologist consideration of experimental design issues and methods for the preparation of RNA samples from a variety of tissue sources suitable for microarray analysis.