This chapter discusses the basic concepts related to transcript analysis. mRNA abundance measurements provide a useful tool to study gene regulation. Currently, most groups use such measurements to investigate the expression of a small number of specific genes. However, with the advent of genomic sequencing projects and the completion of the yeast genome sequence, genomic transcript analyses are being exploited to generate global pictures of gene regulation. By necessity, genome-scale transcript analyses are focusing mainly on the open reading frames (ORFs) themselves—that is, coding sequences. However, the secondary and tertiary structures formed by these sequences and their 5′-leader and 3′-trailer regions exert strong influences on gene expression at post-transcriptional levels. Hence, these issues are an integral part of transcript analysis. The chapter discusses classical methods for the analysis of specific mRNAs. It describes new technologies that are being developed for gene expression analysis and focuses mainly on mRNA abundance measurements. Methods for the analysis of transcript structure and stability are also discussed in the chapter.