Experiments involving high-throughput sequencing are widely used for analyses of chromatin function and gene expression. Common examples are the use of chromatin immunoprecipitation for the analysis of chromatin modifications or factor binding, enzymatic digestions for chromatin structure assays, and RNA sequencing to assess gene expression changes after biological perturbations. To investigate the pattern and abundance of sequence signal across regions of interest, data are typically visualized using aggregate plots or stacked rows of signal in the form of heat maps. We found that available plotting software was either slow and laborious or difficult to use by biologists with little computational training. To address this need, we developed SeqPlots, a user-friendly GUI application that runs on all common operating systems as a web browser application. After selecting sets of signal and feature files and choosing plotting parameters, users can plot of any combination of signal and feature as an aggregate plot or heat map in a matter of seconds simply by clicking a grid. Output is highly configurable and batch operations can generate a large number of plots at once. The design and ease of use of SeqPlots encourages wide data exploration, which should aid the discovery of novel genomic associations.