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Objectives This study aims to analyse the disease composition of primary care visits rather than specialist visits, the former of which had scarcely been studied. We adopted specific disease classification (International Statistical Classification of Diseases and Related Health Problems, 10th Revision), disease system and communicable/non-communicable/injury disease classification, and variations of sex and age were also analysed.Setting We extracted data from all community health service centres (CHSCs) and community health service stations in Pudong, Shanghai, from 2016 to 2018 using the electronic health record systems of the Pudong health information centre.Participants Our data included all 46 720 972 primary care visits from 2016 to 2018 in CHSCs in Pudong.Results We found that the top five diseases in primary care visits continued to be primary hypertension, problems related to medical facilities, chronic ischaemic heart disease, unspecified diabetes mellitus and acute upper respiratory infection. Lipoprotein metabolism disorder visits continued to increase over the study years. The numbers and proportions of patients with hypertension and unspecified diabetes were higher among men than women, and other cerebrovascular diseases were higher among women than men. The top five disease systems were circulatory system diseases, respiratory system diseases, endocrine/nutritional/metabolic diseases, factors influencing health status and digestive system diseases. The rankings of respiratory system and endocrine/nutritional/metabolic diseases rose over time. Non-communicable diseases (NCDs) accounted for approximately 90% of the primary care visits—a much higher percentage than other causes. The top five NCDs in primary care visits were cardiovascular and circulatory diseases, musculoskeletal disorders, diabetes, digestive diseases and urogenital diseases. Compared with women, men suffered from cardiovascular diseases at an earlier age.Conclusions Different from specialist visits, common diseases, especially NCDs, were the main disease composition of current primary healthcare visits while the former focused on intractable diseases such as tumours, indicating that primary healthcare had played the role of gatekeeper of the healthcare system.