Found a rapid increase of HIV infections in persons who inject drugs (PWIDs) in Bulgaria. Two local HIV-1 epidemics among PWIDs in Bulgaria were dominated by non-B subtypes. Identify the origin of the two major HIV-1 clades among PWIDs in Bulgaria. Low drug resistance mutations are present in both treatment experienced and naïve individuals. High prevalence of HBV, HCV and HIV co-infections among PWIDs in Bulgaria.