DHAV-1 infects DEF and miRNAs and mRNA of ducklings.We characterized and compared miRNA and mRNA expression profiles in duck embryonic fibroblasts (DEF) and the liver of ducklings infected with DHAV-1. 130 and 72 differentially expressed (DE) miRNA (DEM),2204 and 1976 differentially expressed (DE) mRNA (DEG) were identified. 15 up-regulated DEM, 5 down-regulated DEM,340 up-regulated DEG, and 50 down-regulated DEG were found in vitro and in vivo DHAV-1 infection. In particular, we identified target genes and functional annotations of DE mRNA in vivo and in vitro infections. We enriched with multiple gene ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, which may have important roles in viral virulence, cell proliferation, and metabolism