Modalities of questionnaire administration may affect data quality, particularly when conducting Biological and Behavioral Surveillance Surveys (BBSS) of uniformed personnel. We aimed to examine differences in administration, reporting and data quality across several common modalities of administration for BBSS endeavors. Prior to a large-scale BBSS endeavor with the uniformed services of Peru, we pilot tested three modes of questionnaire administration among personnel engaged in internal combat: face-to-face interview (FFI), self-administered paper-based interview (SAPI), and audio computer-assisted self-interview (ACASI). Individuals who took the survey using ACASI were less likely to have missing data on measures of sexual risk and alcohol abuse and were more likely to report sexual risk behaviours and symptoms of alcohol abuse; however, more individuals took the survey using SAPI given inadequate time to devote to sitting through an entire FFI or ACASI. Sexually transmitted infections did not vary significantly across modes of questionnaire administration. While more logistically complicated for BBSS efforts in resource-constrained settings, we recommend the use of ACASI in collecting BBSS data from uniformed personnel if conditions are permissible. © The Author(s) 2013 Reprints and permissions: sagepub.co.uk/journalsPermissions.nav.