Research into angiogenesis and vascular microarchitecture has contributed to progress in a wide variety of biomedical fields, but increased understanding is limited, in part, by the available assays and imaging modalities. Techniques that allow quantitation of vascular microarchitecture are needed. A comprehensive method is presented that uses 6-μm-thick serial sections of frozen tissue samples, immunostaining for CD31, brightfield microscopy, automated alignment of two-dimensional serial sections, and volume rendering to produce high-resolution, three-dimensional, quantifiable images of microvascular structure. Application of the technique is shown by characterizing vascularization into a fibrin gel implanted against the skeletal muscle of rats and explanted after 7 days. Comparing measurements from automated and manually aligned MRI and fibrin samples verified quantitation. Automation removes concerns of observer bias or variation inherent in manual alignment and increases the speed of analysis. Analysis of the fibrin gel reveals a dense (4.3 ± 1.1% endothelial cell density) network of tortuous (1.37 ± 0.05 tortuosity) capillaries that replaces the gel as it degrades. There is a high level of void space (22.8 ± 3.6%) in the gel, and average capillary length in the fibrovascular tissue was 93.0 ± 7.4 μm. Data obtained from these automatically aligned images agreed with those obtained using manual analysis (no statistical difference), and the results are consistent with data from traditional methods. © 2002 Elsevier Science (USA).