The aim of the present study was to evaluate the expression of genes in relation to the exploratory activity of rats. Limbic system-associated membrane protein (LsAMP) gene, gamma-aminobutyric acid-(GABA)- and cholecystokinin-(CCK)-related genes were analyzed in the frontal cortex, amygdala and periaqueductal gray (PAG) after exposure of rats to exploratory challenge. Two groups of animals displaying low and high exploratory activity in the elevated plus-maze were selected for gene expression studies from the population of 43 male Wistar rats. Eight rats were taken randomly from the same cages as animals exposed to the plus-maze, but they were not subjected to the exploratory test. This home-cage control group was also used for gene expression analysis in order to explore a possible impact of the plus-maze exposure. Rats with low and high exploratory activity displayed clearly distinct profiles in gene expression. Most prominent alterations were established in the amygdala where almost all GABA-related and CCK receptor genes were two- to five-fold up-regulated in low exploratory activity rats compared to high exploratory activity and home-cage control group. The expression of several GABA-related genes was also increased in the PAG of animals displaying low exploratory activity compared to the other groups. Moreover, we found reduced expression of GABA- and CCK-related genes in all three brain regions in animals with high exploratory activity compared to the home-cage control group. In addition to these findings, we established a significantly increased expression of the LsAMP gene in the amygdala and PAG of low exploratory activity animals compared with the other groups. In conclusion, low and high exploratory activity rats differed not only by their exploratory activity but also displayed opposite gene expression patterns. Low exploratory activity of rats correlated with the up-regulation of LsAMP and GABA-related genes in the amygdala and PAG and with the up-regulation of CCK receptors in the amygdala. High exploratory activity of rats was related to a significant down-regulation of CCK receptor genes in the amygdala and PAG. These rats also displayed the reduced expression of GABA-related genes in the frontal cortex and PAG.