OBJECTIVES: This study explored the prevalence and degree of misalignment between gastroenterologists and people with inflammatory bowel disease (IBD) and investigated communication features related to misalignment. METHODS: A mixed-methods approach incorporated qualitative and quantitative analyses of consultations and post-consultation patient and doctor interviews. Gastroenterologists at two Australian teaching hospitals and IBD patients participated in this study. Doctor-patient misalignment about topics discussed in consultations was quantified using patient and doctor interviews. Predictors of misalignment were hypothesised through a linguistic analysis of consultations and tested quantitatively. RESULTS: Data from 69 patients and seven gastroenterologists showed that consultation participants had different perceptions about at least one aspect of care in 36 % of the consultations. Predictors of misalignment included missing the opportunity to clarify an issue or concern and missing the opportunity to explain the rationale for a diagnosis or recommendation. CONCLUSION: Staying on the topic until the patient is ready to move on and using so-called related messages in questions and explanations increases the likelihood of doctor-patient alignment. PRACTICE IMPLICATIONS: Generic and IBD-specific clinician- and patient-targeted interventions should cover strategies for adequately discussing patients' issues and concerns and clinicians' clinical reasoning. These strategies should also be considered in designing health promotion activities.