Functional magnetic resonance imaging (fMRI) studies consistently demonstrate an enhanced activation of the visual cortex in reaction to emotionally salient visual stimuli. This increase of activation is probably modulated by top-down processes, that are initiated in emotion processing structures, specifically the amygdala and the orbitofrontal cortex. In the present fMRI study, a differential fear conditioning paradigm was applied to investigate this assumed modulation. Hemodynamic responses towards a neutral visual stimulus (CS+) predicting an electrical stimulation (UCS) were compared with responses towards a neutral and unpaired stimulus (CS-). Thereby, particularly the time courses of neural responses were considered. Skin conductance measures were concurrently recorded. Our results show that the differentiation between CS+ and CS- within the amygdala and the extended visual cortex was accomplished during a late acquisition phase. In the orbitofrontal cortex the differentiation occurred at an earlier stage and was then sustained throughout acquisition. It is suggested that these altering activation patterns are reflecting different phases of learning, integrating the analyzed regions to varying degrees. Additionally, the results indicate that statistical analyses comprising a temporal variation of hemodynamic responses are more likely to detect amygdala activation.