Cystic echinococcosis is a major emerging zoonosis in many Eastern European and Asian countries. Post slaughter examinations of 684 pig livers in Lithuania revealed significantly higher numbers of Echinococcus granulosus infections in animals from family farms (13.2%; 95% CI 10.7-16.2) as compared with those from industrial farms (4.1%; 95% CI 0.8-11.5). The prevalence was also significantly higher in pigs older than 1 year than in younger ones. In addition, in 0.5% of the pigs from the family farms, infertile and calcified E. multilocularis lesions were identified by PCR. Faecal samples from rural dogs (n=240) originating from 177 family farms in 12 villages were investigated for taeniid eggs with two methods. Significantly more dogs excreting taeniid eggs were diagnosed with the flotation/sieving method (n=34) as compared to the modified McMaster method (n=12). Multiplex PCR performed with DNA from taeniid eggs isolated from faeces of 34 dogs revealed 26 infections with Taenia spp., 9 with E. granulosus and 2 with E. multilocularis (4 cases with concurrent Taenia spp. and E. granulosus or E. multilocularis infections). Genotyping of E. granulosus cyst tissues from 7 pigs, 1 head of cattle and from E. granulosus eggs from 8 dog faeces revealed the genotype G6/7 ('pig/camel strain') in all cases. The high infection pressure with Echinococcus spp. in family farms necessitates initiating control programs.