The ComplexHeatmap package is introduced for the visualization of multidimensional genomic data. It provides advanced functionalities for customizing heatmaps, arranging multiple parallel heatmaps, and including user-defined annotation graphics. The package allows for the efficient visualization of patterns and correlations among high-dimensional genomic data. It supports flexible clustering, row and column annotations, and interactive selection of heatmaps. The package is implemented in an object-oriented way with a user-friendly API, enabling the generation of novel views of multidimensional datasets. The package is available from Bioconductor and is designed to overcome the limitations of traditional heatmap tools. The package is demonstrated with four real-world datasets, showing its ability to reveal patterns and correlations among multiple sources of information. The package also supports the visualization of complex information, such as the enhanced OncoPrint. The application of ComplexHeatmap is illustrated with examples, including the visualization of genomic alterations and the heterogeneity of mouse T-cells. The package is able to handle complex annotations and is demonstrated with supplementary files showing correlations between methylation, gene expression, enhancers, and gene-related information. The package is supported by the German Cancer Research Center and the BMBF-funded de.NBI HD-HuB network. No conflicts of interest are declared.The ComplexHeatmap package is introduced for the visualization of multidimensional genomic data. It provides advanced functionalities for customizing heatmaps, arranging multiple parallel heatmaps, and including user-defined annotation graphics. The package allows for the efficient visualization of patterns and correlations among high-dimensional genomic data. It supports flexible clustering, row and column annotations, and interactive selection of heatmaps. The package is implemented in an object-oriented way with a user-friendly API, enabling the generation of novel views of multidimensional datasets. The package is available from Bioconductor and is designed to overcome the limitations of traditional heatmap tools. The package is demonstrated with four real-world datasets, showing its ability to reveal patterns and correlations among multiple sources of information. The package also supports the visualization of complex information, such as the enhanced OncoPrint. The application of ComplexHeatmap is illustrated with examples, including the visualization of genomic alterations and the heterogeneity of mouse T-cells. The package is able to handle complex annotations and is demonstrated with supplementary files showing correlations between methylation, gene expression, enhancers, and gene-related information. The package is supported by the German Cancer Research Center and the BMBF-funded de.NBI HD-HuB network. No conflicts of interest are declared.