BACKGROUND: The occurrence of false-positive alerts is an important outcome measure in computer-aided colon polyp detection (CADe) studies. However, there is no consensus definition of a false positive in clinical trials evaluating CADe in colonoscopy. We aimed to study the diagnostic performance of CADe based on different threshold definitions for false-positive alerts. METHODS: A previously validated CADe system was applied to screening/surveillance colonoscopy videos. Different thresholds for false-positive alerts were defined based on the time an alert box was continuously traced by the system. Primary outcomes were false-positive results and specificity using different threshold definitions of false positive. RESULTS: 62 colonoscopies were analyzed. CADe specificity and accuracy were 93.2 % and 97.8 %, respectively, for a threshold definition of ≥ 0.5 seconds, 98.6 % and 99.5 % for a threshold definition of ≥ 1 second, and 99.8 % and 99.9 % for a threshold definition of ≥ 2 seconds. CONCLUSION: Our analysis demonstrated how different threshold definitions of false positive can impact the reported diagnostic performance of CADe for colon polyp detection.