Background: Patient safety research has focused largely on hospital settings despite the fact that in many countries, the majority of patient contacts are in primary care. The knowledge base about patient safety in primary care is developing but sparse and diagnostic error is a relatively understudied and an unmeasured area of patient safety. Diagnostic error rates vary according to how 'error' is defined but one suggested hallmark is clear evidence of 'missed opportunity' (MDOs) makes a correct or timely diagnosis to prevent them. While there is no agreed definition or method of measuring MDOs, retrospective manual chart or patient record reviews are a 'gold standard'. This study protocol aims to (1) determine the incidence of MDOs in English general practice, (2) identify the confounding and contributing factors that lead to MDOs and (3) determine the (potential) impact of the detected MDOs on patients. Methods/Design: We plan to conduct a two-phase retrospective review of electronic health records in the Greater Manchester (GM) area of the UK. In the first phase, clinician reviewers will calibrate their performance in identifying and assessing MDOs against a gold standard 'primary reviewer' through the use of 'double' reviews of records. The findings will enable a preliminary estimate of the incidence of MDOs in general practice, which will be used to calculate the number of records to be reviewed in the second phase in order to estimate the true incidence of MDO in general practice. A sample of 15 general practices is required for phase 1 and up to 35 practices for phase 2. In each practice, the sample will consist of 100 patients aged =18 years on 1 April 2013 who have attended a face-to-face 'index consultation' between 1 April 2013 and 31 March 2015. The index consultation will be selected randomly from each unique patient record, occurring between 1 July 2013 and 30 June 2014. Discussion: There are no reliable estimates of safety problems related to diagnosis in English general practice. This study will lay the foundation for safety improvements in this area by providing a more reliable estimate of MDOs, their impact and their contributory factors.