Background Perceptions of appropriateness of treatments may differ between gastroenterologists (GIs) and inflammatory bowel disease (IBD) patients. The aim of this study was to explore and compare GIs' and patients' perceptions of risks and benefits of treatments and prioritization of expected outcomes. Methods Four vignette cases were drawn from clinical situations and used in three independent focus groups with GIs (n = 7), ulcerative colitis (UC-p, n = 8) and Crohn's disease patients (CD-p, n = 6). Content analysis was performed based on the conversation transcripts. Results UC-p agreed more often with GIs' treatment choices than CD-p. CD-p often considered 5-ASA as a placebo. UC-p saw topical 5-ASA as a temporary solution, neither comfortable nor practical when professionally active. Azathioprine was considered as the treatment for which the risks versus benefits were perceived as the highest. The main risk perceived by patients on anti-TNFs was a potential loss of response. Divergences were observed on 1) stop of treatment: UC-p did not easily concur with stopping a treatment, which differed from GIs' expectation of patients' perceptions; CD-p were more prone to consider stopping treatment than GIs, 2) perception of outcomes: physicians had a focus on long-term objective goals. Patients' expectations were of shorter term and mainly concerned stress management, nutritional advice, and information on the treatments effects. Conclusions Overall, patients and GIs agreed on perceptions of IBD treatments. GIs seemed more concerned about objective and scientific measures of remission whereas patients focused on quality of life and social outcomes when it came to evaluating a therapy.