Abstract Background Disease control relies on pathogen identification and understanding reservoirs. Staphylococcus aureus infection prevention is based upon decades of research on colonization and infection, but diminishing returns from mitigation efforts suggest significant knowledge gaps. Existing knowledge and mitigation protocols are founded upon culture-based detection, with almost no information about pathogen quantities. Methods We used culture and a quantitative polymerase chain reaction assay on samples from 3 body sites to characterize colonization more comprehensively than previous studies by describing both prevalence and pathogen quantity. Results We show a much higher overall prevalence (65.9%) than previously documented, with higher quantities and prevalence associated with the nares, non-Hispanic males (86.9%), and correlating with colonization in other body sites. These results suggest that research and clinical practices likely misclassify over half of colonized persons, limiting mitigation measures and their impact. Conclusions This work begins the process of rebuilding foundational knowledge of S aureus carriage with more accurate and wholistic approaches. Unprecedentedly high community prevalence and assessment of pathogen load provides novel insights into S aureus carriage and suggests that detection and our understanding of carriage may need to be re-evaluated for effective infection mitigation.