The analysis and visualization of arrayed high-throughput screens (HTS), such as cell-based RNAi or small-molecule HTS experiments, requires specialized computational methods. Software packages such as the R/Bioconductor package cellHTS have been developed to support the analysis and are broadly used by the high-throughput screening community. However, exploratory data analysis and integration of screening results remains challenging due to the size of produced data tables in multi-channel experiments and the lack of user-friendly tools to integrate and visualize screening results. Here we present HTSvis, an R/Shiny open-source web application for interactive visualization and exploratory analysis of arrayed high-throughput data. Using a light-weight infrastructure suitable for desktop computers, HTSvis can be used to visualize raw data, perform quality control and interactively visualize screening results from single- to multi-channel measurements, such as image-based, screens. Input data can either be a result file obtained upon analysis with cellHTS or a generic table with raw or analyzed data from, e.g. a high-content microscopy screen. HTSvis can be downloaded from http://github.com/boutroslab/HTSvis.