To further understand the roles of growth factors in the olfactory neurogenesis, we studied the mRNA levels of diverse genes in olfactory bulb (OB) and olfactory epithelium (OE) during the regeneration process of OE. mRNA expression levels of various genes in the OB and OE during the regeneration processes of OE from damage induced by methimazole administration were studied by DNA microarray analysis. The results were confirmed by quantitative real-time RT-PCR and immunohistochemistry. Expression levels of various genes dramatically changed during the observation period. Among them, mRNA expression of BDNF dramatically increased in OE during the first 7 days and then decreased. In contrast, mRNA expression of BDNF in OB significantly decreased during the first 7 days after administration and then gradually increased. The changes in the mRNA levels of OMP in OB precisely followed those of OMP in OE and OB. The present results suggest that BDNF in OE contributes to the early stage of regeneration, and BDNF in OB has its role in the late stage of regeneration of olfactory receptor neurons (ORNs).