The primary focus of this study was to determine if there were differences in the report of health indicators between anonymous and confidential self-report questionnaires. The anonymous and confidential data collection conditions differed in the verbal instructions given before the administration in the classroom and the questionnaire itself. The differences in responses between the two groups were found to be small for most items and scales. It is concluded that in general that confidential administration of these self-report questionnaires renders the same epidemiological results as anonymous administration. The results indicate that the effect of social desirability is not different in the anonymous and confidential condition confirming previous study results. Self-report questionnaires have acquired an accepted role in youth research. They are easy to administer in a group setting and can address a wide range of topics. In the Netherlands, many municipal health services regularly use questionnaires on a variety of topics. However, with the use of anonymous self-reports doubt has been raised as to whether total anonymity affects the results. The Netherlands recently changed from anonymous self-reports to a confidential procedure. The study was conducted in 7 secondary schools in Rotterdam City with an 83 percent response rate (n=704). Questions about social desirability were added to the questionnaire, and the one-way Analysis of Variance was performed to examine the difference in responses of well-being, behavior, and related factors between anonymous and confidential. Tables, references