Giardia duodenalis is a worldwide occurring protozoan with zoonotic potential infecting various mammals including humans. Giardia comprises the zoonotic assemblages A and B and the non-zoonotic assemblages C to H, which are characteristic for different host species. The role of pet animals in the transmission cycle of this parasite is still under debate. In order to identify Giardia assemblages in dogs from South Eastern Europe, 1645 faecal samples of household and shelter dogs from Albania, Bulgaria, Hungary, Macedonia, Romania and Serbia were tested for Giardia coproantigen by enzyme-linked immunosorbent assay (ELISA). DNA was extracted from a subset of 107 faecal samples demonstrating Giardia cysts by direct immunofluorescence assay (IFA) or microscopy (15-22 per country) plus 26 IFA-positive canine faecal samples from Croatia. Multilocus sequence typing with nested PCRs was performed targeting five different gene loci: SSU rRNA, ITS1-5.8S-ITS2, beta giardin (bg), glutamate dehydrogenase (gdh) and triosephosphate isomerase (tpi). In 33.7 % of all dogs, Giardia antigen was detected by coproantigen ELISA. The prevalence was significantly higher in shelter dogs compared to household dogs (57.2 vs. 29.7 %, p < 0.01). The amplification rate at the different gene loci ranged from 1.5 (tpi) to 82.0 % (SSU rRNA). Sequencing of the PCR products revealed the dog-specific assemblages C and D in 50 and 68 samples, respectively. The results demonstrate that G. duodenalis should be considered as a common parasite in dogs from South Eastern Europe. However, there was no evidence for zoonotic Giardia assemblages in the investigated canine subpopulation
