Studies on human brain microcirculation have thus far yielded few quantitative data, preventing the closest possible interpretation of functional imaging methods such as fMRI and PET that necessarily rely on robustly delineated morphology of haemodynamic systems. Inadequate data in this area can lead to severe underestimation of the spatial specificity of the BOLD response. We took thick sections of Indian ink injected human brain and, using confocal laser microscopy and a novel three-dimensional computer-assisted method we extracted and analyzed hundreds of thousands of vascular segments within a large area of cortex. From this database the global densities, the statistical distributions of diameters and lengths were analysed, separating the tree-like and the net-like parts of the microcirculation. Furthermore, our analysis included variations in volume density along the cortical depth and along vectors parallel to the cortical surface. These morphometric parameters are all key requirements for a sound model of cerebral microcirculation.