Expression of the capsid (PORF2) protein of hepatitis E virus (HEV) in mammalian cells results in heterogeneous intracellular processing with a mixture of stable and rapidly degraded forms, which might be expected to influence immune responses to DNA immunisation. Plasmids encoding the N-terminal 22 or 50 amino acids of PORF2 (Sig1 or Sig3, respectively) fused at the N-terminus of the ORF2.1 antigen of HEV (amino acids 394-660 of PORF2) were examined for processing in vitro and antibody responses in vivo, in both rats and sheep. Unmodified ORF2.1 is an unstable cytosolic protein and Sig1-ORF2.1 is a stable membrane-associated protein, whereas Sig3-ORF2.1 demonstrated heterogeneous processing analogous to that of full-length PORF2. After DNA immunisation, Sig1-ORF2.1 demonstrated a 30-fold enhancement of antibody responses in rats compared to untargeted ORF2.1, increasing to more than 200-fold after boosting with recombinant protein, but was ineffective in sheep. In contrast, Sig3-ORF2.1 did not give a significant effect in rats, but demonstrated 4-5-fold enhancement of antibody responses in sheep, and this enhancement was maintained after boosting with recombinant protein. These results suggest that Sig3 in particular may have promise as a targeting molecule for DNA vaccines in large animals.