Health care workers (HCW) have an elevated risk of acquiring and transmitting parenteral infections. The aim of this study was to evaluate the prevalence of hepatitis B virus (HBV) and hepatitis C virus (HCV) markers with the final goal to encourage HBV vaccination of the non-immune Albanian HCW. Among 480 HCW enrolled, 92 were physicians, 246 were nurses/techniques, 120 were auxiliary workers and 22 were office workers. The HBsAg, anti-HBc and anti-HCV prevalence were 8.1%, 70% and 0.6%, respectively. The highest (11.4%) HBsAg prevalence was observed in the youngest age group (20-30 years of age). High HBsAg prevalence (7.2-7.5%) was detected also in age groups above 30 years. The highest HBsAg prevalence (12.6%) was found in the auxiliaries. The anti-HBc prevalence increased significantly with age from 59% in HCWs younger than 39 years to 87% among those older than 50 years. After adjustments for different job categories, age older than 40 years remained independently associated with anti-HBc positivity (OR = 2.9; 95% CI 1.9-4.6) and inversely associated with the lack of HBV immunity or infection markers (OR = 0.4; 95% CI 0.2-0.7). Of 142 HBsAg negative and/or anti-HBc Ab negative sera, 28 (20%) tested positive for anti-HBs. The 114 remaining individuals with no HBV infection or immunity markers were vaccinated against HBV infection. A high HBV infection rate and low HBV vaccination coverage were found in Albanian HCW. Albania is a Mediterranean country still highly endemic for HBV infection and new strategies to promote HBV vaccination are to be adopted.