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Faecal occult blood test (FOBT) screening for colorectal cancer (CRC) is implemented in several countries. Approximately half of all screen positive persons have negative colonoscopy, but consensus is lacking on how these persons should be followed up. Health authorities in Denmark and The Netherlands recommend suspending screening for 8–10 years, while patients in UK are invited to screening after 2 years. In this cohort-study, we followed 166,277 individuals invited to FOBT-screening in 2005–2006 and a reference group comprising the remaining 1,240,348 Danes of the same age. We linked Danish population and health service registers to obtain information about colonoscopy outcome and incident CRC. We estimated CRC risk by colonoscopy outcome (adenoma, other colorectal pathology or negative colonoscopy) for the reference group, the screening group, and subgroups. Persons with positive screening FOBT followed by negative colonoscopy had the same long-term CRC risk as persons with adenoma detected due to a positive screening FOBT (aHR 1.33, 95% CI: 0.65–2.71). We found no difference in the long-term CRC risk between persons with negative colonoscopy after a positive FOBT screening test and the unscreened reference population (aHR 1.05, 95% CI: 0.62–1.78). Since FOBT screen positive persons in our study remained at average risk of CRC despite of a negative index colonoscopy, we question the safety of suspending FOBT screening for this group. It needs to be monitored whether recent efforts to improve colonoscopy quality have been successful in ensuring low CRC risk after negative colonoscopy also in FOBT positive persons.