Microwave synthesis using a domestic microwave oven was first reported by Gedye and Giguere in 1986. Since then, several attempts have been made to apply microwaves to organic synthesis. In the field of positron emission tomography (PET) synthesis, which utilizes nuclides with short half-lives, microwave-assisted radiolabeling reactions have attracted significant attention owing to their successful applications. When microwaves are used as the source of energy, the reactions proceed faster and give higher yields than those performed under conventional thermal conditions. Herein, we briefly describe the characteristics of microwave reactions and their applications in radiolabeling of PET and single-photon emission computed tomography (SPECT) imaging probes. We also summarize the characteristics of commercially available microwave reactors and of resonant-type microwave reactors that we developed in recent studies.