Allows users to interactively visualize their data in the form of heat maps. Heatmapper is designed to be easily used and easily understood by both specialists and non-specialists, alike. Through its intuitive graphical user interface and a large number of example files, Heatmapper allows users to quickly create a wide variety of heat maps for many different data types. These include: (i) pairwise distance maps; (ii) correlation matrices; (iii) image overlay heat maps; (iv) latitude and longitude heat maps; (v) geopolitical (choropleth) heat maps and (vi) expression-based heat maps from transcriptomic, proteomic and metabolomic experiments. Heatmapper offers a number of simple and intuitive customization options for facile adjustments to each heat map's appearance and interactive querying of each heat map's numerical data content. Heat map data can be easily uploaded to Heatmapper in text, Excel or tab delimited formatted tables and the resulting heat map images can be easily downloaded in common formats including PNG, JPG and PDF.