The purpose of this study was to investigate amygdala-related fear and anxiety in two inbred rat lines differing in emotionality (RHA/Verh and RLA/Verh), and to relate the behaviour of the animals to neuronal types in different nuclei of the amygdala. The behavioural tests used were the motility test, elevated plus-maze and fear-potentiated startle response. The neurons investigated were immunoreactive for the anxiogenic peptide corticotropin-releasing factor (CRF-ir), the anxiolytic peptide neuropeptide Y (NPY-ir), and the calcium-binding proteins parvalbumin (PARV-ir) and calbindin (CALB-ir). The NPY-ir, PARV-ir and CALB-ir neurons studied were subpopulations of GABAergic neurons. RLA/Verh rats, which showed a significant fear-potentiation of the acoustic startle response, had more CRF-ir projection neurons in the central nucleus of the amygdala. The same RLA/Verh rats were either less or equally anxious in the motility test (similar to open field) and elevated plus-maze as compared with RHA/Verh rats. In accordance with this behaviour, the RLA/Verh rats had more NPY-ir neurons in the lateral, and more PARV-ir neurons in basal nuclei of the amygdala than RHA/Verh rats, but no differences were detected in the number of CRF-ir and CALB-ir neurons of the basolateral complex. In conclusion, the RLA/Verh rats displayed an opposite behaviour in the fear-potentiated startle model and the exploratory tests measuring anxiety based on choice behaviour. Thus, the anxiogenic systems in the central nucleus and anxiolytic systems in the basolateral complex of the amygdala might be differentially involved in the fear-potentiated startle paradigm and exploratory tests in the Roman rat lines.