Background: The interpretation of indocyanine green (ICG) angiograms is uncertain in many aspects. We performed a study to examine the involvement of the choriocapillaris (CC) in the late phase of ICG angiography. Methods: An animal model of chorioretinal atrophy prepared by means of injection of sodium iodate 4 months previously was used. The findings of ICG angiography and histological analysis were compared. Results: In the late phase of ICG angiography, three fluorescence patterns were observed: the normal region with diffuse ICG fluorescence, a hypofluorescent region with no diffuse fluorescence, and a region with a mixture of hypofluorescence and bright fluorescence. Histological analysis revealed that there were normal CC endothelial cells bearing fenestrae in the region of normal fluorescence. In the region of hypofluorescence, the CC was almost completely obstructed and remnants of capillaries contained thick cytoplasm and lacked fenestrae. In the mixed region of hypofluorescence and bright fluorescence, the CC was partially obstructed and thickened endothelial cells formed intercellular junction complexes by overlapping each other in a complicated manner. Amorphous substances were deposited in some parts of the choroidal interstitium. Conclusion: The CC may play some role in generating diffuse fluorescence in the late phase of ICC angiography, and the findings of hypofluorescence and bright fluorescence may be related to CC obstruction and increased permeability of abnormal vessels, respectively.