PathScore quantifies the level of enrichment of somatic mutations within curated pathways, applying a novel approach that identifies pathways enriched across patients. The application provides several user-friendly, interactive graphic interfaces for data exploration, including tools for comparing pathway effect sizes, significance, gene-set overlap and enrichment differences between projects. Availability and Implementation: Web application available at http://pathscore.publichealth.yale.edu. Site implemented in Python and MySQL, with all major browsers supported. Source code available at http://github.com/sggaffney/pathscore with a GPLv3 license. Supplementary Information: Additional documentation can be found at http://pathscore.publichealth.yale.edu/faq.