We have developed a sensitive method for the detection of specific genes simultaneously. First, DNA was amplified by a novel asymmetric multiplex PCR with universal primer(s). Second, the 6-carboxytetramethylrhodamine (TAMRA)-labeled PCR products were hybridized specifically with oligonucleotide microarrays. Finally, matched duplexes were detected by using a laser induced fluorescence scanner. The usefulness of this method was illustrated by analyzing severe acute respiratory syndrome (SARS) coronavirus RNA. The detection limit was 100 copies/μL. The results of the asymmetric multiplex nested reverse transcription-PCR were in agreement with the results of the microarray hybridization, while no hybridization signal was lost like what has happened with applicons from the symmetric amplifications. This reliable method can be applied to the identification of other microorganisms, screening of the genetic diseases, and other fields.