To assess among parents longitudinal predictors of human papillomavirus (HPV) vaccination uptake for their daughters, random samples of parents were identified via municipal services and sent baseline questionnaires in June 2009 and follow-up questionnaires in November 2011 after their uptake decision. Hierarchical logistic regression analysis was used to assess whether demographic characteristics, and affective and social cognitive factors, predicted uptake at follow-up. Response rates of the baseline and follow-up questionnaire were 29.8% (1762/5918) and 74.3% (793/1067), respectively. Uptake was predicted by a later (2011) versus earlier (2010) decision about uptake as HPV vaccination implementation [odds ratio (OR) 2.48; 95% confidence interval (CI) 1.11-5.52], anticipated regret about no uptake (OR 1.43; 95% CI 1.08-1.89) and intention (OR 2.61; 95% CI 1.47-4.61). There was an interaction between ambivalence and attitude (OR 1.68; 95% CI 1.14-2.47); parents with a positive attitude and a high ambivalence toward vaccination were more likely to have their daughter vaccinated than parents with a positive attitude and a low ambivalence. An informed choice about uptake (5/7 correct items) was made by 44%. In conclusion, uptake was predicted by intention, a later (2011) versus earlier (2010) decision and by anticipated regret about no uptake. Decisions regarding new vaccines are difficult to make, we recommend a well-balanced implementation process.