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Granular corneal dystrophy type 2 (GCD2) causes the formation of corneal deposits having 3 different morphological types. We used Fourier domain optical coherence tomography to assess the depths of each type according to the morphology.A prospective study was performed in 54 eyes of 54 heterozygous patients with GCD2. Corneal deposits of 54 patients with GCD2 were classified into 3 morphological types: type 1, diffuse haze; type 2, granular shape (2 subgroups: type 2a, round granulated and type 2b, round spiculated); and type 3, linear shape (2 subgroups: type 3a, short side branched and type 3b, long side branched). Using Fourier domain optical coherence tomography, we measured the distances from the Bowman layer to the upper surface of the deposits (USBL), to the lower surface of the deposits (LSBL), and the thickness of the deposits (TD). The deposits formed along the flap interface were also examined among 19 patients who had LASIK.Types 1 and 2 deposits were always adjacent to the Bowman layer; thus the USBLs for each were 0.0 ± 0.0 μm, whereas that of type 3 deposits was 65.4 ± 48.0 μm (P < 0.0001). The LSBL and TD of linear deposits with long side branches (type 3) (313.3 ± 71.4 and 246.2 ± 71.9 μm) were greater than those of type 1 (47.7 ± 10.2 and 47.7 ± 10.2 μm) and type 2 (91.3 ± 39.5 and 91.3 ± 39.5 μm) (P < 0.0001). There were no differences in the measurements between the subgroups type 2a and type 2b or between types 3a and 3b. USBL of the laser in situ keratomileusis group was 54.5 ± 29.8 μm.The depths of corneal deposits in patients with GCD2 were associated with the morphology of the deposits. The linear deposits were located most deeply in the cornea, followed by granular deposits and diffuse haze moving anteriorly. Several deposits have distinct depths according to the morphological types.