Background: In the last 20 years, researchers have been using computer self-administered questionnaires to gather data on a wide range of adolescent health related behaviours. More recently, researchers collecting data in schools have started to use smaller hand-held computers for their ease of use and portability. The aim of this study is to describe a new technology with wi-fi enabled hand-held internet tablets and to compare adolescent preferences of laptop computers or hand-held internet tablets in administering a youth health and well-being questionnaire in a school setting. Methods: A total of 177 students took part in a pilot study of a national youth health and wellbeing survey. Students were randomly assigned to internet tablets or laptops at the start of the survey and were changed to the alternate mode of administration about half-way through the questionnaire. Students at the end of the questionnaire were asked which of the two modes of administration (1) they preferred, (2) was easier to use, (3) was more private and confidential, and (4) was easier to answer truthfully. Results: Many students expressed no preference between laptop computers or internet tablets. However, among the students who expressed a preference between laptop computers or internet tablets, the majority of students found the internet tablets more private and confidential (p < 0.001) and easier to answer questions truthfully (p < 0.001) compared to laptop computers. Conclusion: This study demonstrates that using wi-fi enabled hand-held internet tablets is a feasible methodology for school-based surveys especially when asking about sensitive information.