Although the bodies in mammals are seemingly symmetry, there are many asymmetric characters in their functions and/or shapes when we investigate them in detail. For example, it is widely known that the left and right hemispheres of the brain are not equal in its functions. However, little is known about the meaning of such asymmetry. In the present study, as the first step to investigate the functional asymmetry of the amygdala, we observed c-Fos expression in the left and right amygdala in response to the auditory conditioned stimulus (CS) that had been paired with foot shocks. Wistar male rats were fear-conditioned to the CS by receiving the CS and foot shock simultaneously (paired group). We also prepared the subjects that received the same number of CS and foot shocks separately as the control group (unpaired group). Then, 24 hours after the fear conditioning, the subjects in both groups were exposed to the CS during the fear-expression test. After the test, we sampled the brain of the subjects and observed c-Fos expression in the basolateral complex of the amygdala (BLA) and central amygdala (CeA) by immunohistochemistry. During the fear-expression test, the subjects in the paired group showed significantly longer duration of freezing and lower frequency of walking as compared to the subjects in the unpaired group. In addition, the subjects in the paired group showed increased c-Fos expression both in the BLA and CeA as compared to the subjects in the unpaired group. These results suggest that the subjects in the paired group were successfully fear-conditioned to the CS. When we compared the number of c-Fos expressing cells between the left and right hemispheres of the paired group, the number of cells expressing c-Fos in the right CeA is larger than those in the left CeA. However, we did not find the difference between the left and right BLA. Neither did we find any differences in the unpaired group. These results suggest that the right CeA is more strongly activated to the auditory CS than the left CeA. These results suggest the functional asymmetry of the amygdala in rats.