There has been increasing interest in using of web-based surveys--rather than paper based surveys--for collecting data on alcohol and other drug use in middle and high schools in the US. However, prior research has indicated that respondent confidentiality is an underlying concern with online data collection especially when computer-assisted surveys are administered in group settings such as computer labs and classrooms. Using a sample of 341 high school students, we conducted a study comparing alcohol risk behavior prevalence rates from the web-based surveys with paper-form version of the same survey. The online surveys used in the study implemented several programming safeguards to enhance privacy. The goal of our study was to see if the risk-behavior items--when transitioned to an online format with these additional safeguards--would provide prevalence estimates that are comparable to its paper form version. Results showed that overall alcohol prevalence rates did not vary significantly between the two conditions. However, there was a significant interaction between gender and survey mode. Females reported lower mean risk indicator rates compared to males, possibly indicating stronger privacy concerns among the former group. The results suggest that online survey administration may require targeted efforts to help alleviate confidentiality concerns among adolescent girls.