Falah M1, Kavand A2, Yousefi Mashouf R3 1. Professor, Department of Parasitology, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran 2. MSc in Parasitology, Boroujerd Social Security Organization, Boroujerd, Iran 3. Associate Professor, Department of Microbiology, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran Abstract Background: Hydatid cyst, the larval stage or metacestode of Echinococcosis, is an infection caused by cestode species of the genus Echinococcus and often localized in viscera of animals and humans. Hydatid cyst is typically filled with a clear fluid (hydatid fluid) that is sterile bacteriologically. Bacterial infection of hydatid fluid is sometimes present, but not always, and this leads to sterilizing the cyst and prevents producing protoscoleces. In this study the bacterial infection rate of animals hydatid cyst in Hamadan and Boroujerd slaughterhouses were compared. Materials and methods: Referring to Hamadan and Boroujerd slaughterhouses a total of 5709 livestock were inspected for the presence of hydatid cysts. In infected livestock, cyst number, size (diameter), type, and fertility or infertility on the basis of protoscolex presence, and bacterial infection status were determined and recorded. The hydatid fluid of all the collected cysts was cultured separately for isolation and identification of bacterium. Results: Hydatid cysts were found in 6.5% of the animals in Hamadan and in 7% of the animals in Boroujerd. In Hamadan slaughterhouse, only 20% of cysts were fertile and the rest were infertile however, in Boroujerd slaughterhouse, 32% of the cysts were fertile. The isolated bacteria in infected cysts in Hamadan were as bellow: Escherichia coli, Klebsiella, Proteus, Enterobacter, Staphylococci β-hemolytic and non hemolytic, Pseudomonas and Edwardsiella. The most common bacteria in Hamadan were E. coli (23.94%) and Klebsiella (22.5%), and in Boroujerd E. coli (35.7%) and Klebsiella (42.8%). In Boroujerd the rates were 93% and 7% respectively. Conclusion: This study indicated that the infection rate of hydatid cysts was not statistically significant in the two regions of Hamadan and Boroujerd. A high percentage of cysts in both regions were infected bacteriologically.