OBJECTIVE: Determine the prevalence of infections by the hepatitis B (HBV) and C (HCV) viruses and the risk factors associated with their acquisition in clinically healthy military personnel. METHOD: Correlational and analytic transversal study. The population was made up of active, clinically healthy military personnel from the Peruvian Air Force that volunteered for a screening program between October and December 2007. The HBsAg and anti-HBc markers of HBV and the anti-HCV marker of HVC were evaluated. RESULTS: Of the 3,343 military personnel studied, 93.2% (3,116) were male and 6.8% (227) were female, with an average age of 38.9+/-8.6 years (range: 18 to 60 years old), mostly non-commissioned officers (79.5%). An HBsAg prevalence of 0.33% was found, with an anti-HBc prevalence of 0.58%, while the prevalence of anti-HCV was 0.21%. The risk factor associated with active infection by HBV (HBsAG) was risky sexual behavior (OR: 8.3; IC 95%:1.6-42.4 and p=0.01). On the hand, for the past infection by HBV (anti-HBc), the associated risk factors were risky sexual behavior (OR: 6.3; IC 95%:1.7-23.4 and p=0.006) and tattoos (OR: 5.5; IC 95%:1.2-25.8 and p=0.031). No association was found between the risk factors studied and seropositivity by HCV. CONCLUSIONS: We found a low prevalence of the serological markers of infection by hepatitis B and C viruses in active military personnel. The risk factors associated with infection by HBV were risky sexual conduct and the use of tattoos. There was no risk factor found to be associated with infection by HCV in this population.