ABSTRACT. The aim of the study was to investigate the grass carp hemorrhagic infection pathway and its key-related genes. Grass carp reovirus (GCRV) might cause hemorrhagic disease in grass carps. Healthy grass carp fingerlings (N = 60) were divided into control and infected groups. Fish in the control group were intraperitoneally (ip) injected with 0.6% fish physiological saline; the infected group received 5,000,000 50% tissue culture infective doses of GCRV 873 standard strain, a double-stranded RNA (dsRNA) virus strain, ip, in 0.5 mL. Illumina HiSeq TM 2000 was used for transcriptome sequencing, and real-time polymerase chain reaction (PCR) used to detect complement factors II (C2), III (C3), and V (C5); profibrinolysin (PLG); and coagulation factor II (F2) expression. A total of 2,722,223 reads were detected in the control group, and 2,751,111 in the infected group. Among 11,023 unigenes obtained after transcriptome assembly, 10,021 unigenes were significantly differentially expressed. Gene ontology and KEGG analysis, a collection of databases dealing with genomes and biological pathways, were performed to classify unigenes into functional categories, to understand gene function and identify regulatory pathways. Real-time PCR analysis showed that C2, C3, C5, PLG, and F2 expression levels were down-regulated, confirming results of pathway-enrichment analysis. This is the first application of highthroughput sequencing technology to investigate the in vivo effects of GCRV, on genes and pathways involved in the immune response to infection in grass carp.