The present study aims to compare the unwanted intrusions experienced by obsessive–compulsive (OCD) and eating disorder (ED) patients, their appraisals, and their control strategies and analyse which variables predict the intrusions' disruption and emotional disturbance in each group. Seventy‐nine OCD and 177 ED patients completed two equivalent self‐reports designed to assess OCD‐related and ED‐related intrusions, their dysfunctional appraisals, and associated control strategies. OCD and ED patients experienced intrusions with comparable frequency and emotional disturbance, but OCD patients experienced greater disruption. Differences appeared between groups on some appraisals and control strategies. Intolerance to uncertainty (OCD group) and thought importance (ED group) predicted their respective emotional disturbance and disruption. Additionally, control importance (OCD group) and thought–action fusion moral (OCD and ED groups) predicted their emotional disturbance. OCD and ED share the presence of intrusions; however, different variables explain why they are disruptive and emotionally disturbing. Cognitive intrusions require further investigation as a transdiagnostic variable. Copyright © 2014 John Wiley & Sons, Ltd and Eating Disorders Association.