Purpose: To clarify differences between eyes showing hyperautofluorescent choroidal vessels in both nasal and temporal, or only the nasal, portions of the fundus using fundus autofluorescence. Methods: Nineteen eyes with hyperautofluorescent vessels in both nasal and temporal portions (group 1) and 17 only the nasal portion (group 2) of the fundus were studied. Choroidal and retinal thicknesses (foveal, and nasal and temporal 3,000 µm from the fovea), axial length, and refraction were compared between the two groups. Results: In group 1, the average foveal, nasal, and temporal choroidal thicknesses (mean ± SD) were 69.0 ± 30.9, 57.1 ± 18.7, and 88.3 ± 30.4 μm, retinal thicknesses 170.1 ± 48.5, 221.9 ± 46.5, and 209.5 ± 37.9 μm, axial length 28.2 ± 2.2 mm, and refraction -9.9 ± 5.9 dpt. In group 2, the respective values were 174.8 ± 43.0, 80.5 ± 20.9, and 173.5 ± 46.1 μm, 213.4 ± 29.8, 278.3 ± 20.2, and 252.8 ± 19.6 μm, 24.2 ± 1.4 mm, and -1.8 ± 3.8 dpt. There were significant between-group differences for all items (p < 0.05). Conclusions: Fundus autofluorescence tends to be associated with the detection of hyperautofluorescent choroidal vessels in eyes with strong myopia or greater axial length.