PURPOSE: To compare the experiences of perceived stigma (PS) in both patients with irritable bowel syndrome (IBS) and inflammatory bowel disease (IBD) and examine its relationship to patient-reported outcomes in both patient populations. METHODS: IBD and IBS patients were recruited from an outpatient gastroenterology clinic and online via support message boards and classifieds. Participants completed a series of questionnaires to measure the perception of illness stigma, psychological functioning, and clinical and demographic data. RESULTS: Two hundred and sixty-nine IBS and 227 IBD patients participated. IBS patients were more likely to report high levels of perceived stigma across a wider range of sources, with the largest difference being for health care providers. Twenty-seven percent of IBS patients reported moderate to high levels of perceived stigma, compared with 8% of IBD. While perception of stigma was correlated with poorer patient-reported outcomes in both patient groups, correlations were larger for IBD compared with IBS. CONCLUSIONS: This study demonstrates that both IBD and IBS patients perceive stigma about their illness. As demonstrated by increased depression and anxiety, decreased self-esteem and self-efficacy, and lower quality of life in both patient groups, PS was shown to have a negative impact on clinical outcomes.