Functional genomic increasingly requires the cell-specific localization of gene expression. The histological analysis of mRNA expression is performed by in situ hybridization (ISH), whereas proteins are detected by immunohistochemistry. ISH allows the rapid detection of any transcript with the same protocol provided that its cDNA is known. This is an advantage compared to immunohistochemistry, which necessitates the raise of specific antibodies and the test of different procedures depending on the antigens to detect. However, ISH is subject to multiple technical difficulties. We have developed a nonradioactive ISH protocol allowing the simultaneous coupling of immunohistochemistry to follow gene expression at the protein level on the same section as the mRNA detection. This chapter describes the neuronal nitric oxide synthase (nNOS), argininosuccinate synthetase (AS), and argininosuccinate lyase (AL) mRNA expression in the rat brain to illustrate the methods allowing the nonradioactive localization of transcripts by ISH, coupled to immunohistochemistry to identify the specific cell types of central nervous system (CNS) on the same section.