BackgroundWithin the frame of National Epidemiological Surveillance System, family physicians have an obligation to report infections and suspicions cases.The aim of this study was to evaluate the knowledge, attitudes, daily practice and the reporting activities of Hungarian family physicians regarding to infectious diseases.MethodsA self-administered survey was developed, validated and used. The survey was completed by family physicians who had taken part in continuous medical educational programmes of all Hungarian medical faculties. The questionnaire, consisting demographic questions and 10 statements about their reporting habits were completed by 347 doctors, 8% of the total number of family physicians. The data were processed in a cross-sectional design with general linear model.ResultsAccording to the majority of responders, the current reporting system works efficiently. Rural physicians were mainly agreed, that reporting is not a simply obligation, it is a professional task as well. They were less hindered in daily work by reporting activities, waited less for laboratory confirmation before reporting, reported suspicious cases more frequently.Practitioner’s based in urban settlements preferred to await laboratory tests before reporting and were hindered less by failures of the electronic reporting system.Older physicians trusted more in the recent system and they wished to increase the number of reports.Female physicians have higher consciousness in epidemiology. They were mostly in agreement that even severe infectious diseases can be diagnosed at primary care level and their daily practices were less burdened by reporting duties.ConclusionsBoth the epidemiological knowledge of general practitioners’ and the electronic surveillance systems should be improved. There is a need to develope the electronic infrastructure of primary care. More and regular control is also expected by the health care authorities, beside the synthesis of professional and governmental expectations and regulations.Electronic supplementary materialThe online version of this article (10.1186/s12879-018-2948-5) contains supplementary material, which is available to authorized users.