Following infection with hepatitis E virus (HEV), anti-HEV immunoglobulin (Ig) M is thought to develop before anti-HEV IgG and to be a better marker for differentiating between the acute and convalescent phases of infection. In order to select polypeptides for improved detection of anti-HEV IgM, six and three overlapping polypeptides from open reading frames (ORFs) 2 and 3, respectively, of HEV genotypes 1 and 4 were expressed as fusion proteins in Escherichia coli. The reactivities of the polypeptides with anti-HEV IgM were evaluated using immunoblotting and enzyme immunoassays (EIAs). The data indicated that polypeptides from the N-terminus of ORF3 and middle region of ORF2 were weakly or not reactive with anti-HEV IgM, while those from the remaining regions of ORF2 and ORF3 contained reactive epitopes. Anti-HEV IgM against the N- or C-terminus of ORF2 appeared earlier and disappeared faster than that against polypeptides from the C-terminus of ORF3, based on serum samples from rhesus monkeys infected experimentally, and from patients infected naturally, with HEV. The N- and C-terminal polypeptides from ORF2 complemented one another in detecting anti-HEV IgM and EIA sensitivity was improved significantly with a combination of these polypeptides. The reactivities of ORF2 polypeptides from genotypes 1 and 4 were similar but that of ORF3 differed with sera from monkeys infected by the two genotypes. Thus, a combination of N- and C-terminal polypeptides of ORF2 from one genotype may be effective in EIAs to detect anti-HEV IgM.