The aim of a present study was to identify the genes activated or inactivated in the amygdaloid area after the exposure to cat odor. Cat odor exposure was used to induce the ethologically relevant anxiety reaction in male rats. Differential expression of genes was analyzed using the cDNA Representational Difference Analysis (cDNA RDA). Differentially expressed mRNAs were identified by sequencing combined with database search and subsequently verified by dot blot analysis. Exposure of rats to cat odor induced avoidance of odor stimulus and suppressed the exploratory activity of animals. We found that during the cat odor exposure several genes with various functions were activated in the amygdaloid area of rat. Moreover, reverse subtraction resulted in a different set of genes that are inactivated during anxiety response. These genes can be classified according to their function as the neurotransmission related, enzymes, cell cycle regulating proteins and transcription factors. We found that during anxiety response the genes participating directly or indirectly in the synthesis of neurotransmitters (carboxypeptidase E, tyrosine 3-monooxygenase/tryptophan 5-mono-oxygenase activation protein, wolframin) were up regulated. Moreover, a number of genes involved in the signal transduction (Rho GTPase, neurochondrin, Ca/calmodulin-dependent protein kinase) were also activated. Additionally, reverse subtraction in control animals identified several up regulated genes having the antagonistic action to these genes (nischarin, Rab geranylgeranyl transferase). In conclusion, we were able to define the possible pathways linked to the regulation of anxiety response.