© 2019 Acta Ophthalmologica Scandinavica Foundation. Published by John Wiley & Sons Ltd Purpose: Choroideremia is an X-linked retinal disease characterized by early retinal pigment epithelium (RPE) loss and subsequent retinal degeneration. The RPE adopts either a smooth or mottled appearance on fundus autofluorescence (FAF). It is not known how RPE changes predict the health of the overlying ellipsoid zone (EZ). Methods: A retrospective review of FAF and optical coherence tomography (OCT) images from 20 patients with choroideremia was performed. The percentage of intact EZ in each smooth and mottled FAF region was determined using one horizontal trans-foveal OCT section. Results: Fourteen out of 20 patients had distinct smooth and mottled areas in both eyes and were included in the sub-analysis. On average, 62.5 ± 10.1% of the EZ in each smooth region of the right eyes was intact compared to 10.0 ± 4.3% in the mottled areas. The same trend was observed in left eyes: 76.5 ± 7.2% of the EZ was intact in the smooth regions versus 9.8 ± 3.9% in the mottled areas (two-way anova, p < 0.0001). Thus, the mottled FAF regions were associated with EZ disruption more so than the smooth areas. Conclusion: Retinal pigment epithelium (RPE) changes correlate with the health of the overlying EZ in choroideremia. The smooth FAF region likely represents early stages of the disease, with most of the area containing preserved EZ, whereas the mottled zone indicates more advanced stages and has mostly disrupted EZ. Because of the clear relationship between FAF findings and EZ integrity, FAF imaging can be used to monitor disease progression and identify areas of preserved EZ that could be rescued by gene therapy.