Gene expression analysis methods have many applications in the clinical and pharmaceutical fields. They provide tools to determine the effect and side effects of drugs and xenobiotics, and alterations in the physiological state of a cell or tissue under various conditions, among other usages. Here, some of the methods used to quantify gene expression are reviewed. These methods are divided into two groups, those that measure the expression of particular genes, such as northern hybridisation, ribonuclease protection assay, RT-PCR and real-time RT-PCR and those used to measure the expression of a broad-range of genes (mRNA differential display, SAGE and DNA arrays). The potential uses of these methods as well as their advantages and disadvantages are discussed.