Background and Aim: Human papilloma virus-associated anal intraepithelial neoplasia (AIN) precedes most anal cancers and can be detected at colonoscopy. We aimed to quantify AIN detection rates in a general population undergoing colonoscopy. Methods: A retrospective review of a community-based practice for 2 years until December 2019 was conducted. Results: A total of 2525 patients (1051 males and 1474 females; median age 59 years) had 2608 colonoscopies. Ten patients (two males and eight females; median age 57.5 years) had incidentally detected AIN (condyloma acuminatum or AIN1, n = 4; AIN2 or 3, n = 6). AIN was detected in 1 of 261 (95% CI 1/142–1/480) colonoscopies and 1 of 163 (95% CI 1/83–1/321) colonoscopies in women over 40 years old. Conclusions: Opportunistically detecting AIN, especially in women over 40 years old, should be an important adjunct to colonoscopy-based colorectal neoplasia detection.