Bulgaria joined European Union (EU) on 1 January 2007. Since the accession all regulations, directives, decisions, recommendations, and opinions of the European Parliament, the Council of the European Union, and the European Commission are being implemented. The purpose of this study was to present the morbidity of acute hepatitis B virus (HBV) and acute hepatitis C virus (HCV) in Bulgaria before and after accession to the EU. A retrospective study was performed. The morbidity of acute HBV and acute HCV infections in Bulgaria was analyzed over a period of sixteen years (2000-2016). The collected data were based on the National Center of Infectious and Parasitic Diseases (NCIPD) and the National Center of Public Health and Analyses (NCPHA). Between 2000 and 2016, 11038 cases of acute HBV infection and 1681 cases of acute HCV infection were reported in Bulgaria. Before the accession to EU, the morbidity rates of acute HBV and acute HCV infections were 12.77 cases per 100000 population (95% CI: 11.45-13.97) and 1.52 cases per 100000 population (95% CI: 1.17-1.96), respectively. After the accession to the EU, the morbidity rates of acute HBV and acute HCV infections were 5.29 cases per 100000 population (95% CI: 3.86-6.73) and 1.14 cases per 100000 population, respectively. Analysis of the data suggests that there is a tendency for lower morbidity rates of acute HBV. The situation with acute HCV is relatively stable over the years regardless of EU membership.