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Introduction Before publication of the British Society of Gastroenterology and Association of Coloproctology of Great Britain and Ireland guidelines in 2002, screening for people with a family history of colorectal cancer was sporadic and largely dependant on unvalidated local guidelines. Since 1990 we have been screening patients with both high and moderate risk family histories of colorectal cancer using local protocols which were more liberal than the new guidelines. In this study, we have analysed the pathology that would have been missed if we had been using the new guidelines in the period 1990–2002. Method A total of 399 consecutive patients with a positive family history of colorectal malignancy underwent screening endoscopy according to local guidelines. Demographic, endoscopic and pathologic data were prospectively collected. Patients were retrospectively divided into those who would have been screened under the new guidelines (group 1) and those who would not (group 2). The recorded pathology was graded as significant or insignificant and the findings compared between the two groups. Results A total of 399 patients underwent 557 endoscopies of which 278 (50%) were indicated under the new guidelines (group 1) and 279 (50%) were not indicated (group 2). A significant pathology or carcinoma was found in 15.8% of group 1 endoscopies and 10.0% of group 2 endoscopies. This difference was significant. Conclusion If we had been using the new guidelines in the period 1990–2002, we would not have performed 279 (50%) of the 557 procedures, but would not have discovered significant pathology in 10% of the moderate risk endoscopies representing 39% of the significant pathology, which was actually present in this population. [ABSTRACT FROM AUTHOR]