Reports on autochthonous Hepatitis E virus (HEV) infection in humans with genotype 3 assume a zoonotic transmission from domestic pigs. But for domestic pigs only limited information on the seroprevalence of HEV in Germany is available. The aim of this study was to develop an ELISA for the detection of anti-HEV IgG and IgM in porcine serum and meat juice, and furthermore asses the seroprevalence in domestic pigs from Bavaria, Germany. 516 serum samples from pigs and 198 corresponding meat-juice samples from 41 different fattening units were collected in four Bavarian slaughterhouses from august 2009 to february 2010. These samples were tested for anti-HEV antibodies using the newly developed recomWell HEV pig (Mikrogen GmbH, Neuried, Germany) with recombinantly produced antigens of genotype 1 and genotype 3 of HEV. The results were compared to a competitor ELISA (Axiom HEV Ab, Axiom GmbH, Bürstadt, Germany). The data were verified by a HEV line-immunoassay (recomLine HEV, Mikrogen), which also uses antigens of genotype 1 and genotype 3 of HEV. Compared to the line-immunoassay the Mikrogen / Axiom ELISA showed a sensitivity of 90.9% / 95.6% and a specificity of 94.0% / 80.8% respectively. The correlation of optical densities (ODs) between serum and meat-juice was 0.939. Taking all three antibody tests into account, we found an overall anti-HEV IgG seroprevalence of 68.60%. 7.0% of the pigs showed IgM antibodies against HEV. We found a significant difference for two slaughterhouses concerning the seroprevalence rates. One fattening unit was free of antibodies against HEV, nine fattening units showed significant influence on the overall seroprevalence rate. This is the first study showing a (very high) anti-HEV reactivity rate in meat-juice of domestic pigs, which corresponds to the seroprevalences measured consistently by three different assays. A positivity rate of 7.0% for IgM has also never been shown before. The used test-systems seem to be suitable for antibody-testing in blood and meat-juice samples from domestic pigs.