Although face perception is often characterized as depending on holistic, rather than part-based, processing, there is behavioral evidence for independent representations of face parts. Recent work has linked “face-selective” regions defined with functional magnetic resonance imaging (fMRI) to holistic processing, but the response of these areas to face parts remains unclear. Here we examine part-based versus holistic processing in “face-selective” visual areas using face stimuli manipulated in binocular disparity to appear either behind or in front of a set of stripes [Nakayama, K., Shimojo, S., & Silverman, G. H. Stereoscopic depth: Its relation to image segmentation, grouping, and the recognition of occluded objects. Perception, 18, 55–68, 1989]. While the first case will be “filled in” by the visual system and perceived holistically, we demonstrate behaviorally that the latter cannot be completed amodally, and thus is perceived as parts. Using these stimuli in fMRI, we found significant responses to both depth manipulations in inferior occipital gyrus and middle fusiform gyrus (MFG) “face-selective” regions, suggesting that neural populations in these areas encode both parts and wholes. In comparison, applying these depth manipulations to control stimuli (alphanumeric characters) elicited much smaller signal changes within face-selective regions, indicating that the part-based representation for faces is separate from that for objects. The combined adaptation data also showed an interaction of depth and familiarity within the right MFG, with greater adaptation in the back (holistic) condition relative to parts for familiar but not unfamiliar faces. Together, these data indicate that face-selective regions of occipito-temporal cortex engage in both part-based and holistic processing. The relative recruitment of such representations may be additionally influenced by external factors such as familiarity.