Virus infection disrupts the normal metabolism and biological processes of the host. At the molecular level, virus infection triggers a global change in host gene expressions, in particular, the expression changes of host genes that are associated with the stress and defense against pathogen attacks. Thus, studying the alteration of plant gene expression upon virus infection may provide detailed insights into the molecular interaction between virus and host. The real-time fluorescence quantitative PCR (qRT-PCR) has been widely used to investigate the changes in the cellular gene expression. For the accuracy of qRT-PCR analysis,normalization using the appropriate internal control genes is necessary. However, sometimes the expression of housekeeping genes that are commonly used as internal controls is affected by virus infection. In this study, the effect of Rice black-streaked dwarf virus (RBSDV) or Rice stripe virus (RSV) infection on the transcript expression levels of 10 rice (Oryza sativa) housekeeping genes including 18S, 25S, ACT, beta-TUB, eEF-la, eIF-4a, GAPDH, UBC, UBQ-5 and UBQ-10 were assessed by qRT-PCR and then further analyzed by three commonly used algorithms : geNorm, NormFinder and BestKeeper. The qRT-PCR results,combined with three algorithms analyses,revealed that half of the transcript levels of internal control rice genes were affected by RBSDV infection while most of the genes were stable in RSV-infected rice plants. Among those genes, UBC and beta-TUB were the reference genes with the most unaltered transcript levels by infection with RBSDV and RSV. Taken together, our results showed that RBSDV and RSV infections differently affected the transcriptional expression of housekeeping genes that were commonly used for internal control in qRT-PCR. Thus, determining the suitable internal reference genes is crucial for profiling the alteration of gene expression pattern by different virus infections.