mRNA is an important tool to study the effects of particular mutations on the mode of splicing and transcripts. However, it is often difficult to isolate mRNA because the organ or tissue in which the gene is expressed cannot be sampled. We previously identified two probable splicing mutations (c.6485+5G>A and c.8559-2A>G) during the mutation analysis of USH2A in Japanese Usher syndrome (USH) type 2 patients, but we could not observe their effects on splicing because the gene is expressed in only a few tissues/organs, and is not expressed in peripheral lymphocytes. In this study, we used hair roots as a source of mRNA of USH-causing genes, and successfully detected the expression of seven, except USH1C and CLRN1, of the nine USH-causing genes. We used RNA extracted from the hair roots of a patient who has both c.6485+5G>A and c.8559-2A>G mutations in USH2A in a compound heterozygous state to observe the effects of these mutations on transcripts. Reverse-transcription PCR analysis revealed that c.6485+5G>A and c.8559-2A>G inactivated splice donor and splice acceptor sites, respectively, and caused skipping of exons. Thus, RNA extracted from hair roots is a potential powerful and convenient tool for the mutation analysis of USH-causing genes.