The use of hair roots as experimental samples has been a research focus for understanding the effects of spaceflight on astronauts, because it has many advantages, one of which is the fact that hair matrix cells actively divide in a hair follicle and sensitively reflect the physical conditions of the human body. In 2009, a research program focusing on the analysis of astronauts' hairs was initiated to examine the effects of long-term spaceflight on the gene expression and mineral metabolism in the human body. Since the number of samples per astronaut is limited to 5 strands of hairs at each sampling point, due to the ethical viewpoint of astronauts or limited resources in space, it is important to develop an effective method for the molecular analysis of small amounts of hair roots. In this study, mRNA successfully extracted from 1, 5, and 10 hair follicles was amplified and subjected to the DNA microarray analysis to compare the gene expression within subjects. The results indicated that (1) it was possible to perform the genetic analysis on hair samples stored at −80˚C, even without a fixation buffer and (2) the newly modified method of mRNA extraction and analysis was effective in detecting differential gene expression in samples containing only 5 hairs. In conclusion, RNA was efficiently extracted from 5 hair roots, which is the same number of hair roots used in the space experiment; therefore, this method can be applied to genetically analyze astronauts' hair amples. s