Recently, it has been shown in rats that specific characteristics of somatosensory-evoked potentials (SEPs) recorded from different sites on the scalp correlate differently to the amount of unpleasantness experienced by the animal following noxious stimulation. It was shown that the SEP recorded from vertex (Vx-SEP) did correlate with the unpleasantness, whereas the SEP recorded from the primary somatosensory cortex (SI-SEP) did not. In the present study, we further investigated the relationship between the Vx-SEP, SI-SEP and the unpleasantness of noxious stimuli. Therefore, different groups of rats were subjected to a SEP fear-conditioning paradigm in which the unconditioned stimulus (US), represented by noxious stimuli applied to evoke SEPs, was paired to a conditioned stimulus (CS) represented by a tone. Different stimulus intensities of the US were applied in the different groups. After CS-US presentation, CS-induced fear-conditioned behaviour was analysed in relation to the characteristics of the Vx- and SI-SEP during CS-US presentation. Results showed that increasing stimulus intensities led to increased SEP amplitudes, which were paralleled by an increased amount of CS-induced fear-conditioned behaviour. No differences between Vx-SEP and SI-SEP were found. The increase in the SEPs in parallel with the increased amount of fear-induced behaviour further supports the SEP to be a potentially valuable tool for studying acute pain and analgesia in animals.