Comprehensive understanding of the three-dimensional structure of the extracellular matrix (ECM) of the lamina cribrosa is central to understanding its role in health and disease, particularly how changes in configuration might precipitate nerve fibre death in glaucoma. Research until recently has relied almost entirely on light and scanning electron microscopy (SEM) to investigate the ECM of the lamina cribrosa. In this paper, we review the contribution of these methods to current understanding of the three-dimensional structure of the lamina ECM, highlight their potential weaknesses and emphasise that there is still much to be revealed about the structure of the lamina ECM. We then describe our development of confocal microscopy and computer reconstruction as a new and alternative method of investigating the three-dimensional structure of the lamina ECM. We show how optical sectioning allows the confocal microscope to acquire three-dimensional images of the lamina ECM without the degree of tissue disruption associated with preparation for SEM and demonstrate the versatility of analysis of these images by computer reconstructive software. A case is made for confocal microscopy and computer reconstruction contributing to our understanding of this important but complex and delicate structure.