Microarray technology is an exciting and promising tool, and is increasingly employed for studying circadian rhythms. To obtain optimal results from this technology, it is important to perform quality control experiments before engaging in genome-wide expression analysis. In this chapter, we provide an overview of quantitative polymerase chain reaction experiments using the ABI PRISM 7900HT system for quality control of samples, and microarray experiments using the Affymetrix GeneChip system for genome-wide expression analysis.