This chapter is intended as a handbook for anyone interested in using microarrays to study Toll-like receptor (TLR) function or any other biological question. Although microarray technology has developed into a standard tool at many laboratories disposal, most of the actual microarray processing is done by core facilities using highly specialized equipment. This chapter only briefly describes these methods in principle and instead focus on the parts that investigators themselves can influence, such as the experimental design, RNA isolation, statistical analysis, cluster analysis, data visualization, and biological interpretation.