There is debate in cognitive neuroscience whether conscious versus unconscious processing represents a categorical or a quantitative distinction. The purpose of the study was to explore this matter using functional magnetic resonance imaging (fMRI). We first established objective thresholds of the critical temporal parameters for overt and covert presentations of fear and disgust. Next we applied these stimulus parameters in an fMRI experiment to determine whether non-consciously perceived (covert) facial expressions of fear and disgust show the same double dissociation (amygdala response to fear, insula to disgust) observed with consciously perceived (overt) stimuli. A backward masking paradigm was used. In the psychophysics experiment, the following parameters were established: 30-ms target duration for the covert condition, and 170-ms target duration for the overt condition. Results of the block-design fMRI study indicated substantial differences underlying the perception of fearful and disgusted facial expressions, with significant effects of both emotion and target duration. Findings for the overt condition (170 ms) confirm previous evidence of amygdala activation to fearful faces, and insula activation to disgusted faces, and a double dissociation between these two emotions. In the covert condition (30 ms), the amygdala was not activated to fear, nor was the insula activated to disgust. Overall, findings demonstrate significant differences between the neural responses to fear and to disgust, and between the covert presentations of these two emotions. These results therefore suggest distinct neural correlates of conscious and unconscious emotion perception.