Background Drug misuse is a serious public health problem. Evidence from previous epidemiological studies show that GPs are recording drug misuse in electronic patient records (EPR). However, although the recording trends are similar to national surveys, recording rates are much lower. Aim To explore the factors that influence GPs to record drug misuse in the EPR, and to gain a clearer understanding of the gap between the amount of drug misuse recorded in primary care and that in national surveys and other studies. Design and setting A semi-structured qualitative interview study of GPs working in general practices across England. Method Purposive sampling was employed to recruit 12 GPs, both with and without a special interest in drug misuse, from across England. Semi-structured face-to-face interviews were conducted to consider whether and why GPs record drug misuse, which methods GPs use for recording, GPs’ actions if a patient asks for the information not to be recorded, and GPs’ actions if they think a patient misuses drugs but does not disclose the information. Resulting data were analysed using a combination of inductive and deductive thematic analysis. Results The complexity of asking about drug misuse preceded GPs’ decision to record. They described how the context of the general practice protocols, interaction between GP and patient, and the questioning process affected whether, how, and in which circumstances they asked about drug use. This led to GPs making a clinical decision on whether, who, and how to record in the EPR. Conclusion When making decisions about whether or not to record drug misuse, GPs face complex choices. Aside from their own views, they reported feelings of pressure from the general practice environment in which they worked and their clinical commissioning group, as well as government policies.