Background A condition is defined as rare if it affects fewer than 1 in 2000 people in the general population. Limited evidence suggests that care is poorly co-ordinated for people affected by rare conditions. Objectives To investigate if and how care of people with rare conditions is co-ordinated in the UK, and how people affected by rare conditions would like care to be co-ordinated. Design A mixed-methods study comprising (1) a scoping review to develop a definition of co-ordinated care and identify components of co-ordinated care (n = 154 studies); (2) an exploratory qualitative interview study to understand the impact of a lack of co-ordinated care (n = 15 participants); (3) a national survey among people affected by rare conditions of experiences of care co-ordination (n = 1457 participants); (4) a discrete choice experiment of preferences for co-ordination (n = 996 participants); (5) the development of a taxonomy of co-ordinated care for rare conditions (n = 79 participants); and (6) a review of costs of providing co-ordinated care. Setting Health services for people affected by rare conditions, including gatekeeping to social care provision and third-sector care. Participants Adult patients with rare conditions, parents/carers of children or adults with rare conditions and health-care professionals (e.g. doctors, nurses and allied health professionals) involved in the care of people with rare conditions. No limits were set on the rare conditions included or where people live in the UK. Participants were sampled from patient and provider networks and organisations. Results A definition of co-ordinated care for rare conditions was developed. Care for people affected by rare diseases was found to be not well co-ordinated. For example, only 12% of 760 adult patients affected by a rare disease reported that they had a formal care co-ordinator, 32% reported that they attended a specialist centre and 10% reported that they had a care plan. Patients, parents/carers and health-care professionals all would like care to be better co-ordinated, with some differences in preferences reported by patients and parents/carers and those reported by health-care professionals. Our taxonomy of care co-ordination for rare conditions outlined six domains: (1) ways of organising care, (2) ways of organising teams, (3) responsibilities, (4) how often care appointments and co-ordination take place, (5) access to records and (6) mode of communication. Limitations It was not possible to capture the experiences of people affected by every rare condition. Our sampling strategy in the study may have been biased if study participants were systematically different from the population affected by rare conditions. The cost analysis was limited. Conclusions There is evidence of a lack of co-ordinated care for people affected by rare diseases. This can have a negative impact on the physical and mental health of patients and families, and their financial well-being. Future work Further research would be beneficial to develop feasible, clinically effective and cost-effective models of care co-ordination, using the taxonomy developed in this study. Study registration This study is registered as NIHR Clinical Research Network Portfolio reference number 41132, Research Registry reference number research registry6351 and Integrated Research Application System reference number 254400. Funding This project was funded by the National Institute for Health Research (NIHR) Health and Social Care Delivery Research programme and will be published in full in Health and Social Care Delivery Research; Vol. 10, No. 5. See the NIHR Journals Library website for further project information.