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Gene expression microarrays have become a mainstream technology that can provide valuable insight into psychiatric disorders. Gene expression studies in post mortem brain samples of schizophrenia and bipolar disorder have the potential to yield novel clues about the pathophysiology of these complex trait disorders. In the present review, a short introduction of the genetic and molecular background of schizophrenia and bipolar disorder is followed by a discussion of the basic concept and limits of gene expression microarray technology, and the complexities surrounding the analysis of thousands of gene transcripts. Although this review is intended for use in most platforms, it has a particular focus on the commercially available Affymetrix system. Various computer programs and their principal features are discussed, and it is shown how these programs can be applied to reveal a biological context of microarray findings. I will demonstrate how the programs can help to judge the results rather than focus on their statistical principles. The strength of gene array experiments is their emphasis on broad, biological themes, rather than on specific genes, and proper biostatistical approaches are important to ensure reproducibility of the findings. All results should be verified by independent means. This review is intended to help brain researchers who want to apply gene expression microarray technology to conceptualize research strategies and sample analysis.