Background: To prevent the spread of infectious diseases, several state armies implemented obligatory vaccination programs also practiced in the former Yugoslav National Army (YNA). Iatrogenic hepatitis B virus (HBV) transmissions during vaccinations in the armies were well documented, but to the best of our knowledge, no such study has been performed in the former Yugoslavia. Objectives: In the present study, we determined risk factors for acquiring chronic hepatitis B (CHB) infection in patients in Slovenia. This study focused on the detection of a statistically significant risk factor in males, namely “vaccination in the YNA”. Methods: One thousand seven hundred and twenty-nine patients from all Slovenian regions who tested positive for HBV surface antigen (HBsAg) at the national referential laboratory for viral hepatitis diagnostics between January 1997 and December 2010 were included retrospectively. Accordingly, demographic, epidemiological, virological, and clinical data were extracted from the medical documentation and were statistically analyzed. Results: For 1,122 (64.9%) out of 1,729 patients, data regarding risk factors for acquiring HBV infection were available. The risk factor for infection of almost 60% of HBV chronically infected individuals with available data, followed by “HBV infection in the family” (19.8%) and “blood/blood products transfusion before the nineties” (8%) was unknown. Seven males (0.6%) (mean age ± SD, 53.7 ± 4.50 years) reported “vaccination in the YNA” as a risk factor for acquiring chronic HBV infection. “Vaccination in the YNA” was a significant risk factor for CHB infection in men over 46 years of age (P = 0.006). Conclusions: A significant risk factor for infection in Slovenian men over 46 years of age was identified as “vaccination in the YNA”, which is specific to this geographic region and, to the best of our knowledge, has not been previously described in the peer-reviewed literature.