SUMMARY: The visualization and analysis of genomic repeats is typically accomplished using dot plots; however, the emergence of telomere-to-telomere assemblies with multi-megabase repeats requires new visualization strategies. Here, we introduce StainedGlass, which can generate publication-quality figures and interactive visualizations that depict the identity and orientation of multi-megabase tandem repeat structures at a genome-wide scale. The tool can rapidly reveal higher-order structures and improve the inference of evolutionary history for some of the most complex regions of genomes.AVAILABILITY AND IMPLEMENTATION: StainedGlass is implemented using Snakemake and available open source under the MIT license at https://mrvollger.github.io/StainedGlass/.SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.