Differential gene expression profile is a powerful tool to identify changes in cell or tissue trancriptomes, which allows to understanding complex biological process such as oncogenesis, cell differentiation and host immunological response to pathogens, among others. To date, the gold standard technique to compare gene expression profile is micro-array hybridization of a RNA preparation. In recent years technological advances led to a new generation of sequencing methods, which can be explored to uncover the complete content of a cell transcriptome. Such a deep sequencing of a RNA preparation, named RNA-seq, allows to virtually detect the complete RNA content, including low abundant isoforms. The RNA-seq quantitative aspect may be further explored to detect gene differential expression based on a reference genome and gene model. In contrast to micro-arrays, RNA-seq may find a broader range of RNA isoforms as well as novel RNA molecules, and has been gradually substituting micro-arrays to differential gene expression profile. In this chapter we describe how deep sequencing may be used to describe changes in the gene expression profile, its advantages and limitations.