BACKGROUND: In high income countries, vaccine-preventable diseases have been greatly reduced through routine vaccination programs. Despite this success, many parents question, and a small proportion even refuse vaccination for their children. As no qualitative studies have explored the factors behind these decisions among Dutch parents, we performed a study using online focus groups. METHODS: In total, eight online focus groups (n = 60) which included Dutch parents with at least one child, aged 0-4 years, for whom they refused all or part of the vaccinations within the National Immunization Program (NIP). A thematic analysis was performed to explore factors that influenced the parents' decisions to refuse vaccination. RESULTS: Refusal of vaccination was found to reflect multiple factors including family lifestyle; perceptions about the child's body and immune system; perceived risks of disease, vaccine efficacy, and side effects; perceived advantages of experiencing the disease; prior negative experience with vaccination; and social environment. The use of online focus groups proved to be an effective qualitative research method providing meaningful data. CONCLUSION: Information provided by the NIP turned out to be insufficient for this group of parents. More trust in the NIP and deliberate decisions might result from increased parental understanding of lifestyle and disease susceptibility, the impact of vaccinations on the immune system, and the relative risks of diseases and their vaccines. The public health institute should also inform parents that the NIP is recommended but non-mandatory.