Flow cytometry and cell sorting provides unparalleled means for the identification and purification of specific cell types. It is a mature technology having been in existence commercially for the last 25 yr. High-throughput transcriptional profiling methods have emerged relatively recently. These provide the means to characterize efficiently the genome-wide contribution of individual genes to gene expression. A combination of these methods offers the opportunity to explore the relationship between gene expression and the ways in which different cell types are formed and maintained. This chapter provides a review of published methods for analysis of global gene expression within different cell types in complex tissues and organs, and provides practical details concerning microarray fabrication and use based on presynthesized 70-mer oligonucleotide array elements.