Microarray technology is widely used to examine the gene expression profiles of a multitude of cells and tissues. This technology is based on the hybridization of RNA from tissues or cells to either cDNA or oligonucleotides immobilized on a glass chip or, in increasingly rare cases, on a nylon membrane. One of the first experiments in which cDNA clones were arrayed onto a filter, and then hybridized with cell lysates, analyzed the gene expression profiles of colon cancer, and examined the expression of 4000 genes therein (1). Since then, the identification of genes by the Human Genome Project (2) has allowed for the expansion of the number of cDNA clones or oligonucleotides spotted on a single slide. Today, the average commercial microarray contains roughly 20,000 clones or oligonucleotides,many of which are unique. Some companies, such as Agilent Technologies, also make a slide that encompasses genes from the whole genome with over 44,000 genes spotted on their arrays. Obviously, the analysis of so many data can prove quite overwhelming and labor intensive. The purpose of this chapter is to outline the available techniques for microarray data analysis.