Many cells display dramatically different morphologies when migrating in 3D matrices vs. on planar substrata. How these differences arise and the implications they have on cell migration are not well understood. To address these issues, we examined the locomotive structure and behavior of bovine aortic endothelial cells (ECs) either inside 3D collagen gels or on 2D surfaces. Using time-lapse imaging, immunofluorescence, and confocal microscopy, we identified key morphological differences between ECs in 3D collagen gels vs. on 2D substrata, and also demonstrated important functional similarities. In 3D matrices, ECs formed cylindrical branching pseudopodia, while on 2D substrata they formed wide flat lamellae. Three distinct cytoplasmic zones were identified in both conditions: (i) a small, F-actin-rich, rapidly moving peripheral zone, (ii) a larger, more stable, intermediate zone characterized by abundant microtubules and small organelles, and (iii) a locomotively inert central zone rich in microtubules, and containing the larger organelles. There were few differences between 2D and 3D cells in the content and behavior of their peripheral and central zones, whereas major differences were seen in the shape and types of movements displayed by the intermediate zone, which appeared critical in distributing cell-matrix adhesions and directing cytoplasmic flow. This morphological and functional delineation of cytoplasmic zones provides a conceptual framework for understanding differences in the behavior of cells in 3D and 2D environments, and indicates that cytoskeletal structure and dynamics in the relatively uncharacterized intermediate zone may be particularly important in cell motility in general.