Background: Epidemiologic studies of the carcinogenic stomach bacterium Helicobacter pylori have been limited by the lack of noninvasive detection and genotyping methods. We developed a new stool‐based method for detection, quantification, and partial genotyping of H. pylori using droplet digital PCR (ddPCR), which allows for increased sensitivity and absolute quantification by PCR partitioning. Materials and Methods: Stool‐based ddPCR assays for H. pylori 16S gene detection and cagA virulence gene typing were tested using a collection of 50 matched stool and serum samples from Costa Rican volunteers and 29 H. pylori stool antigen‐tested stool samples collected at a US hospital. Results: The stool‐based H. pylori 16S ddPCR assay had a sensitivity of 84% and 100% and a specificity of 100% and 71% compared to serology and stool antigen tests, respectively. The stool‐based cagA genotyping assay detected cagA in 22 (88%) of 25 stools from CagA antibody‐positive individuals and four (16%) of 25 stools from CagA antibody‐negative individuals from Costa Rica. All 26 of these samples had a Western‐type cagA allele. Presence of serum CagA antibodies was correlated with a significantly higher load of H. pylori in the stool. Conclusions: The stool‐based ddPCR assays are a sensitive, noninvasive method for detection, quantification, and partial genotyping of H. pylori. The quantitative nature of ddPCR‐based H. pylori detection revealed significant variation in bacterial load among individuals that correlates with presence of the cagA virulence gene. These stool‐based ddPCR assays will facilitate future population‐based epidemiologic studies of this important human pathogen.