To study the effect of subthreshold transpupillary thermotherapy (TTT) on the retina and experimental choroidal neovascularization (CNV) in the rat. Subthreshold TTT was performed on normal Brown Norway rats or those with krypton laser-induced CNV and appropriate controls with an 810-nm diode laser coupled to a slit lamp. At different intervals after TTT, fundus fluorescence angiography (FFA) and histopathological examinations were performed. Terminal deoxynucleotidyl transferase biotin-dUTP nick end labeling (TUNEL) was used to detect apoptosis. Immunohistochemistry was used to detect heat shock protein 70 (Hsp70) expression. In normal retina, edema and whitening was found on day 1 after TTT. Different degrees of hyperfluorescence could be seen on FFA. Obvious retina damage, especially in the outer layers, was observed by histology in all the lesions that appeared whitened. In the CNV there was congestion and less damage in the overlying retina than in normal retina on day 1 after TTT. Apoptosis was detected in all retinal layers and CNV lesions by TUNEL. In normal eyes, after TTT, Hsp70 expression was increased in the inner layers of the retina and some of the cells in the choroid. Hsp70 was also increased in laser-induced CNV. Two weeks after TTT, the CNV showed a tendency for fibrosis by Masson staining. FFA did not show much change in the CNV lesions 2 weeks after TTT. Subthreshold TTT has adverse effects on the overlying retina and thus is likely to cause significant functional and morphological long-term sequelae. Subthreshold TTT can cause apoptosis in laser-induced CNV in rats.