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Progress in microarray gene expression technology has been complemented by advances in techniques and tools for microarray data analysis. There exist various types of analyses of microarray data and a variety of public tools are available for performing these analyses. Here, we present an overview of three publicly-accessible web-based tools for microarray data analysis; Gene Expression Pattern Analysis Suite (GEPAS), Expression Profiler: Next Generation (EP: NG), and Microarray Data Analysis Web Tool (MIDAW). The discussion particularly focuses on one of the most widely used microarray data analysis techniques known as clustering. Insights are provided on the properties and usefulness of each of the three tools with regard to clustering. For each of the tools, a thorough exploration of the possibilities provided for various clustering techniques is made. In addition, we present a comparison analysis of the performance of the three tools with emphasis on clustering. vi