Domestic chickens are able to distinguish familiar from unfamiliar conspecifics, however the neuronal mechanisms mediating this behaviour are almost unknown. Moreover, the lateralisation of chicks' social recognition has only been investigated at the behavioural level, but not at the neural level. The aim of the present study was to test the hypothesis that exposure to unfamiliar conspecifics will selectively activate septum, hippocampus or nucleus taeniae of the amygdala of young domestic chicks. Moreover we also wanted to test the lateralisation of this response. For this purpose, we used the immediate early gene product c-Fos to map neural activity. Chicks were housed in pairs for one week. At test, either one of the two chicks was exchanged by an unfamiliar individual (experimental 'unfamiliar' group) or the familiar individual was briefly removed and then placed back in its original cage (control 'familiar' group). Analyses of chicks' interactions with the familiar/unfamiliar social companion revealed a higher number of social pecks directed towards unfamiliar individuals, compared to familiar controls. Moreover, in the group exposed to the unfamiliar individual a significantly higher activation was present in the dorsal and ventral septum of the left hemisphere and in the ventral hippocampus of the right hemisphere, compared to the control condition. These effects were neither present in other subareas of hippocampus or septum, nor in the nucleus taeniae of the amygdala. Our study thus indicates selective lateralised involvement of domestic chicks' septal and hippocampal subregions in responses to unfamiliar conspecific.