The MicroArray Explorer (MAExplorer) is an open-source Java-based microarray data-mining tool that is available from the open source Web site as both a ready-to-run program and source code from http://maexplorer.sourceforge.net/. MAExplorer helps analyze expression patterns of individual genes, gene families, and clusters of genes. It is used as a stand-alone Java application and may be used for both ratio and intensity quantified array data (e.g., Cy3/Cy5, Affymetrix, and others). Data-mining sessions may be saved for continuation at later times or shared with collaborators; significant gene subsets, plots, and reports may be saved on the local disk. Extensions, called MAEPlugins, enable users to add new analysis methods and access to new genomic databases as they become available. MAExplorer was implemented in Java so that the same software could run on many platforms (e.g., Windows, MacOS 8/9 and X, Solaris, Linux, and Unix).