Chemotherapy can not be applied for the control of fish viral diseases because viruses depend on host machinery for their replication. Although new control strategies including vaccination are under development, avoidance of virus introduction by rapid and correct diagnosis is the best way of fish viral disease control. Although observation of virus particles with an electron microscope is an easy method for virus detection, it take a few days for the sample preparation. In order to shorten the sample preparation time, microwave radiation was applied in the procedure. With this method, 15 seconds was enough for fixation of virus infected fish samples or cultured cells inoculated with infectious hematopoietic necrosis virus, which takes 2-4 hours with routine methods. Also four minutes was enough for polymerization of embedding resin which takes 24-48 hours with routine methods. Samples prepared with microwave were good enough for direct electron microscopic observation and immunogold labeling assay.