A new method is described for performing fluorescence in situ hybridization (FISH). FISH signals are enhanced by microwave pulses applied during the DNA-DNA hybridization process. It is the first description of FISH with a single/low-copy probe done more efficiently by application of microwave; the latter leads to quick results or enhancement of weak signals. Microwave FISH has been compared systematically with normal FISH, and we could demonstrate the efficiency of microwave irradiation especially in the first 100 min of hybridization.