Previous studies have suggested that providers of alternative medicine may harbour anti-vaccination attitudes and that these attitudes may develop at an early stage in their careers. We further explored this question by conducting a survey to determine the attitudes of students of naturopathic medicine, a growing alternative medicine discipline, towards recommended paediatric vaccines. We sampled all 4 years of students at the Canadian College of Naturopathic Medicine (CCNM) and obtained a response rate of 59.4% (312 of 525). We found that only 12.8% (40 of 312) of the respondents would advise full vaccination; however, 74.4% (232 of 312) of the respondents would advise partial vaccination. Importantly, both willingness to advise full vaccination and trust in public health and conventional medicine decreased in students in the later years of the programme. Our findings suggest that public health and conventional medical supporters of vaccination need to identify mechanisms for engaging in discussion with this population of complementary/alternative medical professionals at an early stage in their careers.