This study examined differences in the appraisal and thought control strategies associated with the perceived control of unwanted sexual and non-sexual intrusive thoughts. Eleven appraisal dimensions, subjective physiological arousal and 10 thought control strategies were measured in 171 university students who were administered the Revised Obsessive Intrusions Inventory-Sex Version, a self-report measure of unwanted intrusive thoughts. Thought-action fusion (TAF) likelihood was a significant unique predictor of the perceived controllability of respondents' most upsetting sexual and non-sexual intrusive thought. Moreover greater subjective physiological arousal was a significant predictor of reduced control over sexual intrusions, whereas worry that one might act on an intrusive thought and greater effort to control the intrusion were significant unique predictors of the control of non-sexual intrusive thoughts. Various thought control strategies were more often used in response to non-sexual than sexual cognitions. The results are discussed in terms of the differential role of various appraisal processes in the control of unwanted sexual and non-sexual thoughts.