Purpose We have previously shown that fundus autofluorescence (FAF) associated with pigmented choroidal lesions can be attributed to mainly lipofuscin (orange pigment) but also to hyperpigmentation, drusen, or fibrous metaplasia. The purpose of this study is to describe the effects of treatment on FAF in choroidal melanomas after plaque radiotherapy alone or in combination with transpupillary thermotherapy (TTT). Methods Retrospective chart review of eight consecutive patients with choroidal melanoma treated with plaque radiotherapy alone or in combination with TTT who underwent FAF photography before and after treatment. The correlation between FAF patterns and foci of orange pigment, hyperpigmentation, drusen, or fibrous metaplasia was evaluated. Results The median follow-up time was 4 (range 2-9) months. Foci of orange pigment and hyperpigmentation became larger and more numerous after treatment. Fibrous metaplasia was also increased. A complete correlation between increased FAF and orange pigment was found in all eight tumours (100%) before and after treatment. No correlation between hyperpigmentation and increased FAF was found before treatment but a partial correlation was found in all eyes after treatment. Before treatment, correlation between fibrous metaplasia was present in three eyes and increased FAF was partial in two eyes with no correlation in one case. After treatment, this correlation was partial in all presenting eyes (7). Conclusions Following treatment, choroidal melanomas may show increased FAF, mainly due to an increase in the amount of lipofuscin (orange pigment) and hyperpigmentation.