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Purpose Serpiginous choroidopathy (SC) is a severe, progressive, bilateral inflammatory disease which produces a serious visual impairment.The most used tool to determine the activity status is fluorescence angiography (FA), but fundus autofluorescence (FAF) has been proposed as an alternative test. The aim of this study is to correlate the activity status disclosed in FA and FAF, and the variations of FAF images in the evolution of the disease. Methods Prospective consecutive case series. Patients with SC or serpiginous‐like lesions of the Ocular Immunology Unit of our hospital were included from July 2009 to July 2010. All patients underwent FAF (Spaide Autofluorescence Filters, Topcon TRC 50IX) and FA (Topcon TRC 50IX). The correlation between FAF and FA and the behaviour of the lesions according with FAF patterns was evaluated by two independent observers Results Nine patients with SC or serpiginous‐like lesions were included. Both eyes were involved in 7 cases. There was a positive correlation between FAF and FA, and also a positive correlation between observers. Attending to the behaviour of the lesions, 3 different patterns of FAF images in SC can be described: Active Inflammatory Status, Inactive Inflammatory Status and Transitional Status. Conclusion FAF may be used as an useful tool for following up patients with SC. It is possible to keep other invasive techniques, such as FA, for cases with suspicious activity disclosed in FAF. [ABSTRACT FROM AUTHOR]