Asymmetric localizations of cellular proteins and mRNAs are important for cell functions such as division, differentiation and development. The localization of specific mRNA generates cell polarity by controlling the translation sites of specific proteins and thereby restricting their locations to appropriate cellular regions. We have previously reported a novel method based on atomic force microscopy (AFM) for examining gene expression in a single living cell without killing or destroying it. An AFM tip was inserted into a living cell to extract mRNAs, which were analyzed after multiplication by RT-PCR and quantitative PCR. By applying this method, in this study we performed quantitative measurement of mRNA at different loci within individual living cells.