BackgroundSince there is no effective treatment or vaccine against the congenital cytomegalovirus (cCMV) infection, knowledge and awareness of medical doctor’s (MDs) especially family doctors are essential for preventive strategies and it also seems to be usually ignored by healthcare providers. Aim of this study was to investigate awareness of MDs about cCMV infection in Iran.MethodsA single page questionnaire was randomly distributed among 450 MDs including general practitioners, pediatricians, gynecologists, internal and other medical specialists concerning of their knowledge in clinical presentation, diagnosis, prevention, prognosis, epidemiology, transmission, and management of cCMV infection. All statistical analyses were performed using SPSS version 16.ResultsMore than half of questionnaire recipients refused to take part in any of the questionnaire items. The most of the respondents were agreed for newborn CMV screening tests and mandatory CMV test for women trying to get pregnant, which, are not routinely tested. The knowledge of general practitioners about cCMV was less than usual. The field of expertise had a profound effect in this survey, but age and gender did not.ConclusionsOur results indicated that the knowledge of cCMV infection, especially among family doctors contains several gaps. Urgent action is required to improve family doctor’s knowledge of CMV infection. Surveys to evaluate CMV awareness among MDs, healthcare professionals and women of childbearing age are proposed.Electronic supplementary materialThe online version of this article (10.1186/s13052-018-0470-4) contains supplementary material, which is available to authorized users.