Human astrovirus (HAstV) is one of the major causes of viral gastroenteritis in infants and young children. However, data on the host response to and pathogenesis of HAstV infection are limited. The primary goal of this study was to identify differentially expressed genes and enriched pathways associated with HAstV infection in human CaCo­-2 cells. The clinical isolates of HAstV were used to infect CaCo-­2 cells and total viral RNAs in the extracellular medium were quantitatively detected. Real­time reverse transcriptase­polymerase chain reaction (RT­-PCR) assay was applied to clearly demonstrate a significant increase in the amount of viral RNAs in the culture supernatant at 9-­24 h post­infection. Finally, RNA sequencing was performed to compare the transcriptomes of CaCo­-2 cells infected with and without a clinically isolated HAstV strain. Statistical analyses on differentially expressed genes revealed that axon guidance and Ras signaling pathways were altered in HAstV­5-­infected CaCo­-2 cells (P<0.05). This is the first report on the deep­-sequencing analysis of transcripts of CaCo-­2 cells infected with HAstV. The data from this study can serve as a basis for future studies of HAstV pathogenesis.