A new method to detect H5 influenza virus using quantum dots (QDs) and magnetic beads (MBs) is described. QDs conjugated with oligonucleotide probes were used to produce fluorescent signals and MBs, that were also conjugated with probes, were used to isolate and concentrate the signals. Target viral RNAs led to a sandwich hybridization between the functionalized QDs and MBs. One-step hybridization facilitated the subtype determination. As little as 0.1 ng viral RNA could be detected.