In visual backward masking, the visibility of a briefly presented visual target is disrupted by a mask that is presented shortly thereafter. The goal of the current study was to identify regions in the human cortex that may provide the neural basis of visual masking. We searched for areas whose activity correlated with perception as we systematically varied the strength of masking. A total of 13 subjects performed a backward masking task during functional magnetic resonance imaging. Target and mask were presented at three delay intervals (34, 68, and 102 msec) and behavioral measures confirmed that the targets were more visible at longer masking intervals. Two sets of regions of interest were identified: Distinct regions in the visual cortex (V1/V2, LO, hMT+) were segregated using scans to localize visual processing drawn from the existing literature. Additional cortical regions were selected in a data-driven approach based on their activity during the backward masking task. For each set, we determined the regions whose magnitude of activation increased at longer masking intervals. Nine of the subjects provided valid behavioral performance data on the visual masking task and imaging data from these subjects were used for subsequent analysis. The scans of visual processing areas identified four regions, including: early visual areas (V1 and V2), the motion-sensitive regions in the lateral occipital (LO) lobe (hMT+), and two components (dorsal and ventral) of the object-sensitive region, LO. Of these, the ventral and dorsal LO regions were sensitive to the strength of the mask. For the data-driven approach, six regions were identified on the basis of a difference map in which all masking intervals were contrasted with rest. These included the inferior parietal, anterior cingulate, precentral, insula, thalamic, and occipital areas. The predicted effects of more activity with weaker masking were seen in the thalamus, inferior parietal, and anterior cingulate. This study isolated three types of visual processing areas. The first included regions that subserve key stages of vision (including object and motion processing). The second type responded to the presentation of briefly presented visual stimuli, regardless of masking interval. The third type (selected from the first two) included regions sensitive to the interval between the target and mask. These latter regions (including ventral LO, inferior parietal, anterior cingulate, and thalamus) may form the neural substrate of backward masking.