The present study was undertaken to characterize more thoroughly aetiological agent of cystic echinococcosis that still represents a health problem in the Slovak Republic. Sequencing of the mitochondrial ND1 gene, Random Amplified Polymorphic DNA (RAPD) analysis and isoenzyme analyses were used to characterize genetically protoscolices of 37 isolates from pigs and cattle and two isolates from humans collected in different regions of the Slovak Republic. Solely the G7 genotype (pig strain) was identified by ND1 sequences in all 14 pigs isolate examined by this method. This genotype was also found in two human patients and in two cattle. The exclusive finding of the G7 variant has implications for the implementation of control strategies given its unique developmental and biological properties. Despite striking morphological variability, a low degree of the intra-strain variability was found in the Slovak Echinococcus granulosus isolates with the genetic methods used. This was particularly associated with the shape and size of hooks, number of testes and shape of ovaries and uterus. GPI and MDH enzymes were found suitable for the discrimination of G7 and G1 (=cosmopolitan sheep strain) variant.