microRNAs (miRNAs) are small, noncoding RNAs which regulate eukaryotic gene expression via RNA interference pathway. Recently, miRNAs have been identified in a number of viruses with current evidence suggesting that they regulate gene expression in both virus and host. This makes viral miRNAs potential targets of clinical intervention, with the possibility of inhibiting aberrant host gene expression associated with the disease. In this study, computational approaches were taken to scan the hepatitis E virus (HEV) genome for putative pre-miRNA molecules, which were then analyzed for the presence of mature miRNAs. The 3′untranslated region (3′-UTR) and 5′-UTR sequences targeted by these miRNAs were identified using Miranda computational tool, followed by the functional annotation of the associated messenger RNAs (mRNAs) using Gene Ontology terms and Kyoto Encyclopaedia of Genes and Genomes pathway analysis. We identified a total of nine viral encoded miRNAs in HEV. After functional annotation, the majority of the viral miRNA targets were found to be associated with cell cycle, cell differentiation, nitrogen compound metabolism, transmembrane transport, and chromosome organization. This in-silico study identified putative viral miRNAs encoded by HEV and their potential human mRNAs targets.These viral miRNAs have the potential to affect host gene expression as well as viral life cycle and pathogenesis and can, therefore, serve as potential therapeutic targets during HEV infection. K E Y W O R D S hepatitis E, microRNA, messenger RNA, RNA interference 1 | BACKGROUND microRNAs (miRNAs) are small, noncoding RNAs that regulate gene expression in eukaryotes. The 60 to 80-nucleotide (nt) precursor miRNA (pre-miRNA) is of intronic origin and is cleaved in the cytoplasm by the RNAse III enzyme Dicer to yield the 21 to 23-nt long miRNA. These miRNAs interact with the multiprotein RNA-induced silencing complex and can bind specific cellular mRNAs based on sequence complementarity. Depending on the extent of complementarity, the translation of the messenger RNA (mRNA) may be reduced or completely silenced, with the mRNA being marked for destruction. 1 While the regulatory function of miRNAs is well documented in eukaryotes, there have not been many reports on virally encoded miRNAs, with preliminary reports identifying miRNAs in herpes simplex virus type 1, human adenovirus, dengue virus, West Nile virus, porcine reproductive and respiratory syndrome virus, and human cytomegalovirus. 2-8 J Med Virol. 2019;91:1545-1552. wileyonlinelibrary.com/journal/jmv