This dataset contains quantitative PCR (qPCR) laboratory results for Strongyloides stercoralis from biobanked stool samples collected during baseline (pre-intervention) assessments of the DeWorm3 community-based cluster randomised trial. Samples were collected from two sites: Tamil Nadu, India (6,091 samples) and Mangochi, Malawi (4,234 samples) during 2017-2018. Demographic, socioeconomic, and environmental data collected during baseline census and surveys used for this analysis are hosted separately at https://doi.org/10.25934/PR00010754.