Heat maps use color to visually summarize information and make the relationship between data values immediately apparent. Heatmapper is a free data visualization tool that allows users to generate, cluster, and visualize five different types of heat maps: Expression, Pairwise, Image Overlay, Geomap, and Geocoordinate. Users upload their own data and can easily customize their heat map's appearance and plotting parameters. The tool can also be applied to explore datasets using the searchable and sortable data table view, or by hovering the cursor over the heat map to view numeric data values. For detailed information, example images, and instructions on making each of the five classes of heat maps, users can click the "About" drop-down menu at the top of the page and select "Instructions." Sample datasets are provided to experiment with each type of heat map. Heatmapper was developed by the Wishart Research Group at the University of Alberta, with financial support provided by the Canadian Institutes of Health Research (CIHR) and Genome Alberta.