Purpose To assess whether the scores of an Internet-administered adolescent health questionnaire (using two different interfaces) are equivalent to those obtained via paper and pencil (P&P). Furthermore, it compares adolescents’ evaluations of modes of administration. Methods We randomly assigned 591 adolescents (aged 13–17 years) from five secondary schools within their classes to one of the two Internet interfaces (multiple items vs. one item per screen) or P&P. Adolescents completed questionnaires on psychosocial well-being (KIVPA), self-reported problems, health care utilization, and health-related behavior and supplementary evaluation surveys (on the given health questionnaire mode) in the computer classrooms. Differences in questionnaire scores among administration modes were analyzed by the Student’s t-test and Wald test. Results Response rate was 96% (n = 565). Adolescents in the Internet one-item mode more frequently reported satisfaction with appearance compared with the Internet multiple-items mode (p ≤ .01). The Internet group had more adolescents reporting that they have a sufficient number of friends than those in the paper mode (p ≤ .01). The Internet mode received more favorable evaluations than P&P. The multiple items per screen format was favored over the one item per screen format on perceived speed of the administration mode. Conclusions Health questionnaires via Internet were positively evaluated and generally resulted in equal scores of health status/health behavior compared with the P&P mode. We recommend further research with other questionnaires, and in other settings as well with regard to score equivalence between web-based and P&P-administered questionnaires.