Background The 3-dimensional (D) structural abnormalities of the coronary capillary network and capillary volume changes after myocardial reperfusion were investigated using confocal laser scanning microscopy. Methods and Results Using open-chest anesthetized rats' hearts, the left anterior descending artery (LAD) was occluded for 7 min followed by reperfusion. The hearts were divided into 2 groups: (1) reperfused area stained well by intravenous indocyanine green after reperfusion (Reflow), and (2) lack of staining in the reperfused area (No-reflow). The entire coronary microvasculature was filled with contrast medium using a Langendorff's perfusion system. Capillaries were observed 3-dimensionally in the control and reperfused areas in both the Reflow and No-reflow group and the capillary volume fraction was computed from the 3-D images. The reperfused area in both groups showed decreased capillary diameter with waving and shrinkage configuration. In the No-reflow group, marked interruption of capillary network was observed. In the Reflow group the capillary volume fraction was significantly reduced in the reperfused area compared with the control area (14.8±4.1% vs 22.2±5.6%, p<0.05). Capillary volume fraction was further decreased in the No-reflow group compared with Reflow (5.3±1.4% vs 14.8±4.1%, p<0.01). Conclusion The morphological changes in coronary capillaries after reperfusion were characterized by waving and shrinkage, which resulted in a reduction in capillary volume. (Circ J 2004; 68: 868 - 872)