A cross-sectional survey was conducted to estimate the prevalence of Echinococcus multilocularis and E. granulosus infections in domestic dogs and cats from Germany and other European countries. Faecal samples of 21,588 dogs and 10,650 cats routinely submitted to a private veterinary laboratory between June 2004 and June 2005 were examined using the ZnSO(4)-NaCl flotation method. Taeniid eggs were detected in 54 (0.25%) and 37 (0.34%) of the canine and feline faecal samples, respectively. Taeniid eggs were separated and subjected to a DNA preparation and a modified two-step PCR for the detection of Echinococcus spp. based on mitochondrial 12S rRNA genes. PCR products from Echinococcus-negative but cestode-positive reactions were cloned and sequenced to determine the Taenia species. E. multilocularis DNA was specifically amplified in 43 (0.24%) and 25 (0.23%) of the samples from dogs and cats, respectively. E. granulosus DNA was not detected in any sample, while, E. multilocularis-positive samples were detected in dogs from Germany only, those of cats originated from Germany, Denmark and The Netherlands. The prevalence of E. multilocularis egg-positive canine samples was significantly higher in southern (0.35%) than in northern Germany (0.13%). In contrast, no significant regional difference was observed in cats from Germany. Taeniid eggs from Echinococcus-negative samples and from a few samples with macroscopically detected Taenia sp. proglottids were identified as eggs of T. crassiceps (n=8), T. martis, T. serialis, T. polyacantha, T. taeniaeformis and T. pisiformis in dogs (n=1 of each) and T. taeniaeformis (n=11) in cats. The spectrum of cestodes detected in domestic dogs and cats indicate the consumption of small rodents as infection source. The high proportion of E. multilocularis-positive samples, suggest domestic dogs and cats as a possible source of E. multilocularis infection for humans.