As part of an evaluation of the introductory campaign of human papilloma virus (HPV) vaccine in a Scottish health board, self-administered questionnaires were offered to all 5007 eligible girls in school following the third dose of HPV to identify side-effects, reasons for non-vaccination and future cervical screening intentions, and 2775 (56.2%) replied. In all, 630 (23.5%) of vaccinated girls reported side effects to the vaccination, about half of which were common injection-site reactions. Main reported reasons for non-vaccination related to perceived inadequate evidence for HPV safety and efficacy, and lack of perceived need or desire to be vaccinated. A total of 2430 (89.2%) of the girls expressed plans to take up cervical screening when older. Reasons for not planning to take up cervical smear were lack of knowledge about cervical screening, anticipated discomfort or embarrassment with the process and no perceived need for a cervical smear. Unvaccinated girls were less likely to report planning to attend for cervical smears in later life (Yates chi-square = 24.30, p < 0.001). The findings emphasise the importance of information on safety and efficacy in future communications about HPV with schoolage girls. The relationship between vaccination and screening intention, and its implications for widening the gap in health inequalities, also requires careful attention in local implementation of the national HPV vaccination programme.