The oral health habits of pupils had not yet been analyzed for the canton of Neuchâtel. A questionnaire was provided to 9th grade high school pupils (final year) of the three schools located in the Neuchâtel area to asses both oral health knowledge and habits in this connection. The average age was 15.5 ± 0.8 years, and 78.1 % of the questionnaires were returned. The prophylaxis program was conducted for a total of 4.5 h during pupils’ entire time at school. The results sho wed that both knowledge and oral health habits could be improved. As a positive outcome, 99 % of the pupils brush their teeth before going to bed. Comparisons with similar 10-year-old studies from other cantons (Bern, Vaud) showed major differences in knowledge, for example on the importance of fluoridation. Only 54 % of the pupils in Neuchâtel knew that fluoride offers some protection against caries, in spite of the fact that 89% thought that brushing with fluoridated toothpaste protects against caries. Most of the pupils used a fluoridated toothpaste. Furthermore, we found that self-reported sugar consumption was correlated with caries experience, but brushing frequency was not. We recommend introducing a review course for pupils in their last school year, in order to practice interdental cleaning, redefine appropriate, tooth-friendly snacks, and emphasize the importance of regular dental check-ups.