Although aberrant crypt foci (ACF) are estimated to have potential usefulness as a biomarker for colorectal carcinoma (CRC), this remains uncertain because the natural history of ACF has not been well-clarified. To determine the usefulness of ACF as a surrogate marker for CRC, it is necessary to understand the natural history of ACF. A total of 82 subjects who underwent total colonoscopy and whose ACF number was examined at least 2 times at Yokohama City University Hospital were enrolled. We retrospectively evaluated the changes in the ACF number at four different surveillance periods (6 months, 1 year, 2 years, 3 years) and in groups with and without colorectal neoplasms. Furthermore, we classified the subjects into an increased ACF group and a no change/decreased ACF group, and investigated the relationship between the changes in the ACF number and known risk factors for CRC. No significant differences were observed in the ACF number between the first and second observations in any surveillance period groups, and in the groups classified according to the presence or absence of colorectal neoplasms. There were no significant differences between the increased and no change/decreased ACF group in terms of gender, smoking habit, current alcohol consumption, age, BMI, HbA1c or serum triglyceride level (TG), whereas a significant difference between the groups was observed in the serum total cholesterol level (TC) (p=0.012). ACF are a reliable surrogate marker that are not affected by any risk factors for adenomas or CRC, except TC, and may therefore be considered as a useful marker in chemopreventive trials.