Between July 2005 and January 2006 we evaluated 1248 Paraguayan active duty military volunteers. Participants provided a blood sample for HIV testing and answered an anonymous survey. HIV seroprevalence was 0.4% (5 of 1248) among participants. The median age at first sexual intercourse was 16 years. Only 14.8% of participants reported condom use with every sexual encounter. Military students used condoms the most. Participants older than 45 years, compared with younger participants, had a fourfold (adjusted odds ratio 4.3) increased risk of not using condoms. Men were less likely to use a condom, more likely to practice anal intercourse, and had more sexual partners than women. Officers and non-commissioned officers were identified to have a twofold (as measured by adjusted odds ratio = 2.00 and 2.22, respectively) increased risk of having more than two sexual partners in the last month compared with students. Both officers and non-commissioned officers were twice as likely as students to practice anal intercourse. Despite the high-risk behaviours reported by those surveyed, HIV seroprevalence in active duty personnel was low. Future efforts should emphasize on the correct condom use keeping focus on the high-risk behaviours of groups at risk, and on routinely testing the military personnel for HIV.