Background Stool-based screening with Fecal Immunochemical (FIT) or multi-target-stool DNA (mt-sDNA) tests is associated with increased colonoscopy polyp yield. Mt-sDNA includes methylated markers which improve detection of serrated polyps (SP) versus FIT. We compared SP detection in colonoscopies performed for positive FIT or mt-sDNA tests, as well as in colonoscopies without a preceding stool test, using the New Hampshire Colonoscopy Registry, a comprehensive statewide population-based registry. Methods Across the three groups, we compared the frequency of clinically relevant SPs (CRSPs: sessile SPs, hyperplastic polyps ≥10 mm, and traditional serrated adenomas). We also compared SP size, histology, number and bulk (combined sizes). Results Our sample included 560 mt-sDNA+ (age ± SD 66.5 ± 7.9), 414 FIT+ (66.3 ± 8.8) and 59,438 colonoscopy-only patients (61.7 ± 8.0). Mt-sDNA+ patients were more likely to have a higher yield of CRSPs and CRSP bulk than FIT+ (p < 0.0001) or colonoscopy-only patients (p < 0.0001). More mt-sDNA+ patients had CRSPs without large adenomas or CRCs (17.9% vs 9.9% of FIT+ and 8% of colonoscopy-only patients). After adjusting for synchronous large adenomas, CRCs, and other risk factors, mt-sDNA+ patients were more likely (OR 1.82, 95% CI 1.18 – 2.85) than FIT+ patients to have CRSPs. Conclusions Mt-sDNA+ patients had a higher SP yield than FIT+ or colonoscopy-only patients, particularly in the absence of synchronous large adenomas or CRC. Impact Our results suggest that screening with mt-sDNA tests could improve CRC screening by identifying more patients at increased risk from the serrated pathway.