We developed a novel automated system of NAT (nucleic acid amplification technology) based infectious disease testing. The system consists of the automated nucleic acid extractor using the manual DNA/RNA extraction kit‘ EX TRAGEN’ as the reagent and the fluorescence real-time monitor of the TRC (transcription- reverse transcription concerted) amplification in the presence of the INAF (intercalation-activating fluorescence) DNA probe. The present system was applied to the detection of methicillin-resistant Staphylococcus aureus (MRSA) and demonstrated that the nucleic acids were extracted from as much as 32 specimens within 30 minutes, and 10 copies of the target RNA, mRNA of mecA gene, was detected and quantified in 10 minutes.