PRINCIPLES: Children whose parents use complementary and alternative medicine (CAM) often show a lower rate of vaccination than those of parents favouring conventional medicine. We have investigated whether this applies to the paediatric patients presenting to an emergency department in German-speaking Switzerland, where popularity of CAM is rather high. METHODS: A cross-sectional survey was performed of paediatric patients presenting to an urban, tertiary paediatric emergency department. 1007 (63%) of the distributed 1600 questionnaires were available for analysis. RESULTS: 12.7% of all respondents reported refusing some basic vaccination: 3.9% because of recommendation of the physician, 8.7% despite their physician's recommendation. Socio-demographic characterisation of the group of patients refusing vaccination showed older age of children, higher proportion of girls, more single-mothers families and decreased household income. Refusal of basic vaccination was significantly more frequent among CAM-users than among non-users (18.2% versus 3.5%, p <0.001). The highest frequencies of refusal were reported by patients who consulted physicians practicing herbal medicine, anthroposophical medicine or homeopathy. Users and non-users of CAM however, showed comparable rates of immunisation in the case of the vaccinations against invasive meningococcal, pneumococcal disease and flu. Surprisingly, the rate for vaccination against tick-borne encephalitis was higher in the CAM-users group than among the non-users (21.2% versus 15.4%, p <0.05). CONCLUSIONS: A considerable proportion of the study population did not fully accept basic vaccinations. Refusal to follow the basic vaccination schemata was more frequent among CAM-users than non-users and reflected in most cases parental wishes rather than physicians' recommendations.