Cell-directed deposition of aligned collagen fibrils during corneal embryogenesis is poorly understood, despite the fact that it is the basis for the formation of a corneal stroma that must be transparent to visible light and biomechanically stable. Previous studies of the structural development of the specialized matrix in the cornea have been restricted to examinations of tissue sections by conventional light or electron microscopy. Here, we use volume scanning electron microscopy, with sequential removal of ultrathin surface tissue sections achieved either by ablation with a focused ion beam or by serial block face diamond knife microtomy, to examine the microanatomy of the cornea in three dimensions and in large tissue volumes. The results show that corneal keratocytes occupy a significantly greater tissue volume than was previously thought, and there is a clear orthogonality in cell and matrix organization, quantifiable by Fourier analysis. Three-dimensional reconstructions reveal actin-associated tubular cell protrusions, reminiscent of filopodia, but extending more than 30 μm into the extracellular space. The highly extended network of these membrane-bound structures mirrors the alignment of collagen bundles and emergent lamellae and, we propose, plays a fundamental role in dictating the orientation of collagen in the developing cornea.C onnective tissues fulfill diverse functions but conform to a general structural plan of cells surrounded by an extracellular matrix in which collagen is the main structural element (1, 2). Composition and tissue-specific organization of the component collagen fibrils are considered to be critically important for the functional properties of any particular tissue. The unique transparent quality of the cornea arises from its remarkably ordered architecture of aligned and regularly spaced fibrils with a small, consistent diameter (∼30 nm), which are arranged, not into fibers or fascicles as in most other tissues but in superimposed, flattened layers, or lamellae. Lamellae and their component collagen fibrils exhibit preferential orientations throughout the corneal thickness (3), which appear to be closely related to the biomechanical loads to which the tissue is subjected. In adult vertebrates, lamellae traverse the full diameter of the cornea for most of its thickness, and in the avian eye-the subject of most developmental studies-undergo a gradual rotation in their orientation with depth (4). Individual collagen fibrils within midstromal lamellae also appear to traverse the entire diameter of the cornea, a distance of ∼11 mm in adult human eyes. The extraordinary level of order in matrix organization within a hierarchy of fibril, lamella, and stroma overall appears to reflect a considerable level of regulatory influence presumably involving both cell activity and intermolecular interactions.Collagen fibrils exhibit a microfibrillar substructure (5-7), undergoing self-assembly spontaneously in vitro from soluble monomeric collagen in a process largely dependent upon the phy...