BACKGROUND: The purpose of this research is to develop and evaluate methods for conducting cluster randomised trials in a primary care database that contains electronic patient records for large numbers of family practices. Cluster randomised trials are trials in which the units allocated represent groups of individuals, in this case family practices and their registered patients. Cluster randomised trials often suffer from the limitation that they include too few clusters, leading to problems of insufficient power and only imprecise estimation of the intraclass correlation coefficient, a key design parameter. This difficulty might be overcome by utilising databases that already hold electronic patient records for large numbers of practices. The protocol describes one application: a study of antibiotic prescribing for acute respiratory infection; a second protocol outlines an intervention in a less frequent chronic condition of public health importance, stroke. METHODS/DESIGN: The objective of the study is to implement a cluster randomised trial to test the effectiveness of an electronic record-based intervention at achieving a reduction in antibiotic prescribing at consultations for respiratory illness in patients aged 18 and 59 years old in intervention family practices as compared with controls. Family practices will be recruited from the practices that presently contribute data to the UK General Practice Research Database (GPRD). Following randomisation, electronic prompts will be installed remotely at intervention practices to promote adherence with evidence-based standards of medical practice. The intervention was developed through qualitative research at non-intervention practices. Data for outcome assessment will be obtained from anonymised electronic patient records that are routinely collected into GPRD. This protocol outlines the proposed study designs, data sources, sample size requirements, analysis methods and dissemination plans. Ethical issues are also discussed. DISCUSSION: Results from this study will provide methodological evidence concerning the use of electronic patient records and databases for implementing cluster randomised trials in primary care. The study will also provide substantive findings in respect of electronic record-based interventions to reduce antibiotic prescribing in primary care. TRIAL REGISTRATION: Current Controlled Trials ISRCTN 47558792.