To investigate the comparability of health behavior data obtained from adolescents via notebook computer versus those obtained via written questionnaire. We interviewed adolescent patients (ages 13-20 years) receiving services at community adolescent health clinics. Participants anonymously completed either a computer-assisted self-interview (CASI) or a self-administered questionnaire (SAQ), both assessing health-protective behaviors, substance use (i.e., tobacco, alcohol, marijuana) and sexual behaviors. From a pool of 671 adolescent participants (348 completing CASI, 323 completing SAQ), we matched 194 SAQ participants with 194 CASI participants on the basis of gender and race. We could not match individually on the basis of age, but were able to match each gender-race subgroup by mean age. Across the majority of health behaviors (i.e., all health-protective behaviors, tobacco use, sexual behaviors), mode of administration made no significant difference in the reporting of information by adolescents. However, girls reported a greater frequency of alcohol use and marijuana use on CASI than on SAQ, whereas boys reported a lower frequency of alcohol use and marijuana use on CASI than on SAQ. The findings of this study suggest that there may be gender-related differences between modes of anonymous collection of specific adolescent health behaviors such as alcohol and marijuana use. Future studies should incorporate direct questions regarding adolescents' attitude and comfort levels toward completing different modes of data collection.