Background: Research often neglects important gaps in existing evidence. Throughout health care, clinicians and patients face avoidable ‘clinical uncertainties’ daily, making decisions about treatments without reliable evidence about their effectiveness. Objectives: This partnership of UK patients and clinicians had several objectives: 1) developing and implementing a clinician-patient research prioritization methodology; 2) identifying and prioritizing ‘clinical uncertainties’ relating to treatment of urinary incontinence (UI); and 3) promoting clinically useful research. Methods: UK clinician and patient organisations whose remit includes UI were invited to participate. Participating organisations consulted memberships to identify ‘uncertainties’ affecting treatment decisions. ‘Uncertainties’ were also identified in systematic reviews’ research recommendations. Prioritization involved two phases: 1) shortlisting of ‘uncertainties’ by organisations; and 2) patient-clinician prioritisation meeting using established consensus methods. Prioritized ‘uncertainties’ were verified by checking that no relevant up-to-date systematic review of evidence was published. Results: Thirty organisations were invited; 8 patient and 13 clinician organisations participated. Consultation generated 417 perceived ‘uncertainties’, research recommendations 131. Appropriate refining, excluding and combining produced a list of 226 (79 from patients; 37 from clinicians; 102 form research recommendations; 8 from multiple sources). Initial prioritisation shortlisted 29 ‘uncertainties’. Prioritization meeting produced a ‘top ten’ (5 submitted by clinicians, 4 by patients, 1 from research recommendations). Conclusions: The partnership successfully developed and tested a systematic and transparent methodology for patient-clinician consultation and consensus. This can inform future work, which might address limitations and challenges identified. Through consensus, unanswered research questions of importance to patients and clinicians were identified and prioritised. The final list reflects the heterogeneity of populations, treatments and evidence needs associated with UI. Some prioritized ‘uncertainties’ relate to treatments that are widely used yet not thoroughly understood, some to access to care, some to precise surgical research questions. Applications for funding to address some prioritised ‘uncertainties’ are in preparation: proposals range from systematic reviewing to primary research.