Introduction We aimed to identify modifiable risk factors in primary care associated with emergency hospital admissions with Chronic Obstructive Pulmonary Disease in Lothian, Scotland. We sought permission to obtain data from primary to secondary care databases in a way that would allow the required analyses while ensuring that patient confidentiality was protected.

Methods The research protocol proposed an “anonymised linkage” method that linked personal identifiers and pseudonymised them before adding clinical data. All identifiers would be removed from the final analysis dataset. Consent to participate in the project was sought from general practitioners. General information was available to patients about secondary uses of their personal data. Ethical approval was sought from relevant local to national committees.

Results Conflicting views were expressed by different ethical committees. Some took the view that individual patient consent was required for the proposed approach while others viewed it as anonymous database research.

Conclusions In large epidemiological studies it may not be practicable to obtain individual patient consent. UK law and professional guidance supports the use of patient data for research without consent in some circumstances provided the research is deemed to be in the public interest. Data linkage is a powerful tool increasingly used for epidemiological research. However, its use to improve health in Scotland is hampered by lack of clear guidance and inconsistent interpretation. While it is important that patient confidentiality is respected, a balance needs to be struck to enable use of patient data to improve health and the quality of care.