There is currently no widely recognised methodology for undertaking data quality assessment in electronic health records used for research. In an attempt to address this, we have developed a protocol for measuring and monitoring data quality in primary care research databases, whereby practice-based data quality measures are tailored to the intended use of the data. Our approach was informed by an in-depth investigation of aspects of data quality in the Clinical Practice Research Datalink Gold database and presentations of the results to data users. Although based on a primary care database, much of our proposed approach would be equally applicable to other health care databases.