Few studies compare fecal immunochemical test (FIT) and multi-target stool DNA (mt-sDNA) outcomes in practice. We compared colonoscopy yield following FIT+ or mt-sDNA+ tests to colonoscopies without preceding stool tests in the comprehensive population-based New Hampshire Colonoscopy Registry (NHCR). Outcomes were any neoplasia and an ordered outcome: adenocarcinoma, advanced neoplasia (adenoma/serrated polyp {greater than or equal to} 1 cm/villous/high-grade dysplasia), non-advanced neoplasia or normal. Our total sample included 306 mt-sDNA+ (average age +/- SD 67.0 +/- 7.9), 276 FIT+ (66.6 +/- 8.7) and 50,990 colonoscopy-only patients (61.8 +/- 8.1). Among average risk patients (N=240 mt-sDNA+, N=194 FIT+ , N=26,221 colonoscopy only), mt-sDNA+ patients had a higher risk for any neoplasia (67.1%) compared to FIT+ (54.6%, p=0.00098) or colonoscopy (40.8%, p < 0.0001). Severity of findings and histology subtypes differed across the three groups (p<0.0001 for both), with a higher yield of advanced findings in mt-sDNA+ patients. In particular, clinically relevant serrated polyps (hyperplastic polyps {greater than or equal to} 10 mm/traditional serrated adenomas/sessile serrated polyps) were detected at a higher frequency in mt-sDNA+ patients as compared to FIT+ or colonoscopy only patients. Even after adjustment, patients with positive mt-sDNA+ (OR=2.82; 95%CI: 2.00-4.02) or FIT+ tests (OR=1.67; 95% CI: 1.19-2.36) were more likely to have histologically more advanced findings than colonoscopy alone. At follow-up colonoscopy, mt-sDNA+ tests were more likely to predict neoplasia than FIT+, largely due to increased detection of serrated polyps.