The generation of large volumes of omics data to conduct exploratory studies has become feasible and is now extensively used to gain new insights in life sciences. The effective exploration of the generated data by experts is a crucial step for the successful extraction of knowledge from these datasets. This requires availability of intuitive and interactive visualization tools that can display complex data. Matrix heatmaps are graphical representations frequently used for the description of complex omics data. Here, we present jHeatmap, a web-based tool that allows interactive matrix heatmap visualization and exploration. It is an adaptable javascript library designed to be embedded by means of basic coding skills into web portals to visualize data matrices as interactive and customizable heatmaps.