The ability to monitor gene expression in experimental and clinical samples is an essential element of modern molecular biology and cell biology research. However with the advent of a systems biology approach toward understanding cell and cancer biology, analysis of expression of a single gene is no longer desirable. Today, multiplex analysis, where the expression of 8–100 genes can be monitored in one sample, has become a routine aspect of gene expression analysis. In this chapter the various assays systems commercially available for multiplex analysis of both RNA and protein will be discussed.