Prior behavioral studies suggested that global perception of compound stimuli is modulated by the way the local elements are grouped into global structures. The current work examined whether distinct neural mechanisms are involved in global/local processing of compound stimuli when local elements are grouped into global shapes by proximity or by shape similarity. Functional magnetic resonance imaging (fMRI) was used to measure neural activities associated with global/local processing of compound shapes that were presented against either a black background (Experiment 1) or a background of crosses (Experiment 2) while subjects discriminated close or open shapes at the global or local level. Global processing induced activation in the medial occipital cortex in Experiment 1 but in the right inferior temporal, superior parietal, and inferior frontal cortex, and the left inferior parietal gyrus in Experiment 2. Local processing was associated with activations in the left precentral gyrus and right superior temporal gurys in Experiment 1 but in the left posterior inferior parietal gyrus in Experiment 2. The fMRI results suggest that global perception is mediated by distinct neural substrates depending upon how local elements are grouped into global structures.