OBJECTIVES: Many patients experience complex disease courses raising concerns about fragmentation of care and continuity. The objective of the present study was to explore which dimensions that are important to patients in their experience of continuity of care. Patients’ preferences were elicited using a discrete choice experiment (DCE). METHODS: 1800 patients were invited to participate in a postal survey including three patient groups; diabetics, heart patients and cancer patients. Random samples of each of the defined patient groups were recruited through Odense University Hospital given at least one admission during the last two years. The DCE contained five attributes; 1) Involvement of GP in the patient’s course of disease; 2) Arrangement of a contact person at the hospital; 3) Involvement of the patient in the decisions; 4) Yearly consultation at hospital; and 5) Distance to hospital. RESULTS: Data was collected in the period April-June 2009 and resulted in an overall response rate of 67%. Primary analyses of DCE data are promising. All respondents value patient involvement in the treatment decision highly whereas the involvement of GPs matters less - in particular to diabetic patients and cancer patients. We observe some differences in preferences among diabetes compared to the two other patient groups. Notably heart and cancer patients find the offer of yearly consultation unimportant and find the arrangement of a contact person objectionable. These two differences likely indicate patients’ (dis)satisfaction with the health care system and the current organisation of treatment and as such may reflect some lack of continuity of care. CONCLUSIONS: Worldwide there has been a policy focus on enhancing patients’ satisfaction and enhancing continuity of care among patients. The present study contributes to this work by examining what dimensions that are deemed important by patients in their experience with the health care system during their disease courses.