In recent years, DNA microarray has become increasingly popular as a tool to investigate global expression patterns compared to differential display RT-PCR. Although differential display RT-PCR can be labour-intensive, it has its own merits over those of DNA microarray. While the latter usually consists of a well-defined set of species-specific genes, differential display RT-PCR allows the investigation of host-microbe interactions without bias towards any mRNA transcripts. This means that the regulated transcript expression of both host and pathogen can be analysed simultaneously. In addition, novel transcripts and alternate splicing variants pertaining to the infection can also be discovered. We have investigated the response of rhabdomyosarcoma cells to infection with a neurovirulent strain of enterovirus 71 (EV71) at different time-points during the infection process compared with uninfected cells. Using differential display RT-PCR, we identified mRNAs that were up- or down-regulated. Less than half of the clones match known genes including those involved in mediating the cytoskeleton, cell cycle, cell death, protein translational machinery and cellular transport. The rest of the clones do not match any known genes, of which several are novel genes. Noteworthy is the discovery of an alternate splicing form of TRIP7, which is down-regulated during EV71 infection. The differential display technique has potentially wide applicability to elucidate the gene expression or transcriptomic profiles of host-microbe interactions, which can provide a better understanding of microbial pathogenesis.