We describe a method to visualize green fluorescent protein (GFP)-labeled cells in intact organs through combined confocal and reflected laser light imaging. This method allows us a three-dimensional (3-D) view of specific cell types in situ. Imaging of tissues from transgenic mice in which the endothelial cells are labeled with GFP under the control of endothelial-specific tyrosine receptor kinase 2 (TIE2) shows the spatial distribution of the GFP-labeled endothelial cells in intact organs. We have used this method to examine the tissue necrosis in the intact heart and kidney resulting from myocardial and renal infarction. In myocardial infarction produced by surgically occluding the left anterior descending coronary artery, the border of the infarct was highly cellular and showed a disrupted endothelial network and scar tissue appearing as a dense layer of reflection. The induced renal infarction produced by ligating the renal artery in the pedicle showed a clear infarct border in the affected kidney. The 3-D reconstruction of specific cell types in the context of the surrounding tissues should be useful for studying the overall organization and the relationship between different structures in the intact organ in normal and disease states.