Despite several studies conducted to determine the genotypes of cystic echinococcosis (CE) agents in humans and other intermediate hosts, the relationship between parasite genotype and clinical presentation of hydatidosis is yet to be well defined. The aim of this study was to compare the genotypes/haplotypes of CE agents of human extra-hepatopulmonary hydatid cysts and common hydatid cysts of the liver. A comparative analysis was carried out between partial cox1 sequences of ten extra-hepatopulmonary hydatid cysts, two liver cysts and reliable sequences from the GenBank database. All the studied hydatid cysts had the Echinococcus granulosus sensu stricto (G1-G2-G3) genotypes. The liver CE cysts were caused by common G1 genotype, while six of the extra-hepatopulmonary cysts had genotypes different from common G1 cysts. The sequences of these six isolates were identical to the G2 and G3 genotypes of E. granulosus sensu stricto; the kidney and peritoneum cysts and most of the brain cysts were identified as G2 genotype, while G3 genotype was only reported in a cyst belonging to the pelvic region. Given the observed differences between the sequences of hydatid cysts, it seems that the replacement of hydatid cysts in organs other than the liver and lungs can be related to their genotypes and probably intra-genotypic characteristics. It was hypothesized that in each geographic area, less frequent genotypes were likely to be more consistent with placement in the host's unusual organs.