Background: Diagnosis and treatment of bipolar disorder is complex. Health care is supported by clinical guidelines, which are highly based on scientific evidence. However, such care does not necessarily correspond to preferred care according to patients. In order to narrow the gap between scientifically based guidelines and the patient's perceptions of the best clinical practice, additional research is needed. The aim of this study was to create a patient based research agenda for bipolar disorder to enhance the alignment between patients’ needs and care system. Methods: A mixed method study design was employed consisting of two phases: consultation and prioritization. In the consultation phase, six focus group discussions with patients (n = 35) were conducted to explore research needs according to patients, resulting in 23 research topics. Subsequently, these topics were prioritized by means of a questionnaire with patients (n = 219). Results: Patients with bipolar disorder mentioned a variety of research topics covered by the following five themes: causes of disorder; pharmacotherapy; non-pharmacological treatment; diagnosis; and recovery & recovery oriented care. ‘Etiology’ was the topic with highest priority. Discussion: The theme ‘causes of disorder’ is prioritized highest. We argue that this can be explained by the added value of an explanatory framework for appropriate treatment and recovery. The theme ‘recovery & recovery oriented care’ is currently underrepresented in actual research. It is argued that in order to bridge the knowledge and implementation gap, social science and health system research is needed in addition to biomedical research.