The traditional approach to molecular biology consists of studying a small number of genes or proteins that are related to a single biochemical process or pathway. A major paradigm shift recently occurred with the introduction of gene-expression microarrays that measure the expression levels of thousands of genes at once. These comprehensive snapshots of gene activity can be used to investigate metabolic pathways, identify drug targets, and improve disease diagnosis. However, the sheer amount of data obtained using high throughput microarray experiments and the complexity of the existing relevant biological knowledge is beyond the scope of manual analysis. Thus, the bioinformatics algorithms that help analyze such data are a very valuable tool for biomedical science. First, a brief overview of the microarray technology and concepts that are important for understanding the remaining sections are described. Second, microarray data preprocessing, an important topic that has drawn as much attention from the research community as the data analysis itself is discussed. Finally, some of the more important methods for microarray data analysis are described and illustrated with examples and case studies.