Heatmapper is a freely available web server designed to facilitate the creation and visualization of heat maps for various data types and applications. Unlike existing non-commercial heat map packages, Heatmapper offers a versatile and user-friendly interface that supports a wide range of heat map types, including expression-based, pairwise distance, correlation, image overlay, latitude and longitude, and geopolitical (choropleth) heat maps. The tool allows users to generate, cluster, and visualize data, with intuitive customization options for adjusting the appearance and plotting parameters of heat maps. Users can interactively explore data by hovering over cells or using a searchable/sortable data table. Heatmapper supports data upload in text, Excel, or tab-delimited formats, and heat map images can be downloaded in common formats such as PNG, JPG, and PDF. The platform is designed to appeal to a broad audience, including scientists from various fields such as molecular biology, structural biology, epidemiology, environmental science, and more. Heatmapper is accessible at http://www.heatmapper.ca.Heatmapper is a freely available web server designed to facilitate the creation and visualization of heat maps for various data types and applications. Unlike existing non-commercial heat map packages, Heatmapper offers a versatile and user-friendly interface that supports a wide range of heat map types, including expression-based, pairwise distance, correlation, image overlay, latitude and longitude, and geopolitical (choropleth) heat maps. The tool allows users to generate, cluster, and visualize data, with intuitive customization options for adjusting the appearance and plotting parameters of heat maps. Users can interactively explore data by hovering over cells or using a searchable/sortable data table. Heatmapper supports data upload in text, Excel, or tab-delimited formats, and heat map images can be downloaded in common formats such as PNG, JPG, and PDF. The platform is designed to appeal to a broad audience, including scientists from various fields such as molecular biology, structural biology, epidemiology, environmental science, and more. Heatmapper is accessible at http://www.heatmapper.ca.