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Nonpolypoid colorectal neoplasms (NP-CRNs) are more likely to contain high-grade dysplasia or early-stage cancer than polypoid neoplasms. We aimed to determine the long-term outcomes of patients with at least 1 NP-CRN.We performed a longitudinal cohort study of 4454 patients at a Veterans' Affairs hospital who underwent colonoscopy from 2000 through 2005; 341 were found to have 1 or more NP-CRNs and were matched (3:1) with patients found to have 1 or more polypoid neoplasms (controls, n = 1025). We collected and analyzed data on baseline colonoscopy findings and first follow-up colonoscopy results through August 2014. We calculated the incidence of advanced neoplasia at first follow-up colonoscopy, as defined by the presence of ≥1 tubular or sessile serrated adenomas ≥10 mm in diameter, tubulovillous adenoma, high-grade dysplasia, or invasive cancer.A significantly higher proportion of patients with 1 or more NP-CRNs (16.0%) were found to have advanced neoplasia at their first follow-up colonoscopy than controls (8.6%); the adjusted risk ratio was 1.6 (95% confidence interval, 1.05–2.6;P= .03). A significantly higher proportion of patients with 1 or more NP-CRNs were found to have additional NP-CRNs at the follow-up colonoscopy (17%) than controls (7%; relative risk, 2.3; 95% confidence interval, 1.5–3.5;P< .001). Similar proportions of patients in each group developed cancers after colonoscopy.In a longitudinal cohort study, we found that patients with NP-CRN were more likely to develop additional NP-CRNs and to have advanced neoplasms at their first follow-up colonoscopy than patients with only polypoid neoplasms. However, patients with NP-CRN were not more likely to develop cancers after colonoscopy when surveillance guidelines were followed. Larger studies are needed to determine risk of colorectal cancer in patients with NP-CRN.