BackgroundThe UK is dependent on international doctors, with a greater proportion of non-UK qualified doctors working in its universal health care system than in any other European country, except Ireland and Norway. The terms of the UK exit from the European Union can reduce the ability of European Economic Area (EEA) qualified doctors to work in the UK, while new visa requirements will significantly restrict the influx of non-EEA doctors. We aimed to explore the implications of policy restrictions on immigration, by regionally and spatially describing the characteristics of general practitioners (GPs) by region of medical qualification and the characteristics of the populations they serve.MethodsThis is a cross-sectional study on 37,792 of 41,865 GPs in England, as of 30 September 2016. The study involved age, sex, full-time equivalent (FTE), country and region of qualification and geography (organisational regions) of individual GPs. Additionally at the practice and geography levels, we studied patient list size by age groups, average patient location deprivation, the overall morbidity as measured by the Quality and Outcomes Framework (QOF) and the average payment made to primary care per patient.ResultsNon-UK qualified GPs comprised 21.1% of the total numbers of GPs, with the largest percentage observed in East England (29.8%). Compared to UK qualified GPs, EEA and elsewhere qualified GPs had higher FTE (medians were 0.80, 0.89 and 0.93, respectively) and worked in practices with higher median patient location deprivation (18.3, 22.5 and 25.2, respectively). Practices with high percentages of EEA and elsewhere qualified GPs served patients who resided in more deprived areas, had lower GP-to-patient ratios and lower GP-to-cumulative QOF register ratios. A decrease in pay as the percentage of elsewhere qualified GPs increased was observed; a 10% increase in elsewhere qualified GPs was linked to a £1 decrease (95% confidence interval 0.5–1.4) in average pay per patient.ConclusionsA large percentage of the UK general practice workforce consists of non-UK qualified GPs who work longer hours, are older and serve a larger number of patients in more deprived areas. Following Brexit, difficulties in replacing this valuable workforce will primarily threaten the care delivery in deprived areas.Electronic supplementary materialThe online version of this article (doi:10.1186/s12916-017-0953-y) contains supplementary material, which is available to authorized users.