Objectives Countries generally present their overall use of antibiotics as an indicator of antibiotic prescribing quality. Additional insight is urgently needed for targeted improvement recommendations: first, data on specific clinical indications for which antibiotics are used, and second, on distinguishing whether changes in patient consultation or changes in physician prescribing drive changing antibiotic use for particular indications. The aim of this study was to describe the antibiotic management of infectious diseases in the clinical context, by analysing prescribing by physicians and patient consultation incidences per indication over time. Methods A database with all contact data for infectious diseases from 45 primary care practices in the Netherlands (2007–10) was used. Consultation incidences, prescribing rates and choice of antibiotic were analysed per International Classification of Primary Care (ICPC) chapter and relevant ICPC codes. Results Antibiotics were prescribed in ∼25% of infectious disease episodes, mainly respiratory infections, urinary infections and ear and skin infections. Overall, this resulted in 300 prescribed courses of antibiotics per 1000 patient–years. Given a stable prescription rate, a 19% increase in the number of consultations explained the increased antibiotic prescribing for urinary tract infections. Given a stable consultation incidence, an 8% reduction in prescribing rate explained the decreased antibiotic prescribing for respiratory tract infections. Macrolides were predominantly prescribed for respiratory disease (∼66%), amoxicillin/clavulanate for respiratory disease (∼42%) and urinary illness (∼25%), and fluoroquinolones for urinary and genital indications. Conclusions Insight into the reasons for the decreased prescribing for respiratory tract infections and the increased prescribing for urinary tract infections was provided by a detailed analysis of incidences and prescribing rates. For respiratory disease, the second- and third-choice antibiotics were overused. ...