BACKGROUND: The Extended Prostate Cancer Index Composite (EPIC) instrument is a commonly used patient reported outcome (PRO) tool in prostate cancer clinical trials. Summary scores for EPIC subscales are calculated by averaging patient scores for attributes (e.g., side effects), implying equal weighting of the attributes in the absence of evidence showing otherwise. METHODS: We estimated patient preferences for each of the attributes included in the bowel subscale of the EPIC instrument using best-worst (B-W) scaling among a cohort of men with prostate cancer. Patients were presented with multiple tasks in which they were asked to indicate which attribute they would find most and least bothersome at different levels of severity. Analysis utilized both (simple) B-W counts and scores to estimate patient preferences for each attribute as well as attribute levels. RESULTS: A total of 174 respondents from two institutions participated in the survey. Preference estimates for each of the five attributes included in the EPIC-26 bowel subscale showed wide variation preferences: 'losing control of bowel movements' was found to be the most bothersome attribute, with a B-W score of -0.48, followed by bowel urgency which also had negative B-W score (-0.04). Increased frequency of bowel movements was the least bothersome attribute, with a B-W score of +0.33, followed by bloody stools (+0.12), and pelvic/rectal pain (+0.06). Analysis of preference weights for attribute bother levels showed preference estimates be linear. CONCLUSIONS: We provide novel evidence on patient preferences for side effect reduction following prostate radiotherapy. Within the bowel sub-scale of the EPIC-26 short form, we found that bowel incontinence was perceived to be the most bothersome treatment effect, while increased bowel frequency was least bothersome to patients.