A method was successfully developed for the measurement of the virus-infected region and distribution of virus. The system consists of a in situ PCR instrument, a light microscope, and an image processing and analysis software. Through developing a in situ RT-PCR system for location of a strawberry virus, the sections were observed on a Nikon light microscope by magnifying 400×. Alcian blue precipitate was observed in palisade tissues, and it indicated that the virus was located in the tissue. The area of the virus-infected region was measured by NIS-Elements software. At last, the distribution of virus in tissue and the area of infected region could be analyzed and accounted on the basis of the micro-measured results. The average area of forty virus-infected regions was 1.5×103 µm2, in addition, the ratio of the area of healthy region to virus-infected one was 3.4. The system achieved to measure quantitatively the virus-infected tissues dispensing with the complicated transmission electron microscope (TEM).