Background: Combining existing data on background characteristics with data from immunization registers might give insight into determinants of vaccine uptake, which can help to improve communication strategies and invitation policy of National Immunisation Programmes. Methods: The study population consisted of children born in 2005 as registered in the Dutch national immunization register Præventis. A hierarchical logistic regression model was used to quantify associations between individual vaccination status and proxy variables for ethnic background (individual level), socio-economic status (postcode level) and religious objection to vaccination (municipal level). Results: Most children whose both parents were not born in The Netherlands had a somewhat lower full vaccine uptake, for example, children whose both parents were born in Turkey [odds ratio = 0.7 (0.6–0.8)] or in Morocco [odds ratio = 0.8 (0.7–0.9)]. The partial uptake was also relatively high (3.7–8.0%) compared with children whose both parents were born in The Netherlands (3.1%). Municipalities with higher religious objection to vaccination and postcode areas with lower socio-economic status were also associated with a lower full uptake. Conclusions: Despite the high vaccination coverage in The Netherlands, we were able to identify determinants of vaccine uptake by combining existing data sets. This might be an example for other countries. The impact of ethnic background and socio-economic status is not as well known in The Netherlands as the effect of religious objection to vaccination, and deserves more attention. Groups that have a relatively high partial uptake deserve special attention because they do not reject vaccination in general.