Elongated axial length of the eye increases the morbidity of glaucoma. Myopia also associates with elongated axial length, and such ellipsoid shape of the eyeball strongly contributes its pathogenesis. Morphological features of the eyeballs, which could be important factors for developing glaucoma, have not been well described. The aim of this study was to investigate the three-dimensional (3D) topographic features of glaucomatous eyeballs with/without myopia to evaluate the potential of those features for predicting glaucoma. Using a 3.0-tesla MRI, volume-isotropic turbo-spin-echo acquisition T2-weighted images were obtained from 55 patients with glaucoma and 22 controls to delineate the eyeballs. Eyeball volumes, axial lengths and transverse lengths were semi-automatically calculated and compared between four groups: normal, myopia, glaucoma, and glaucoma with myopia. Both glaucoma and myopia increased the eyeball volume compared to the normal eyes. An increased anisotropy ratio (axial/transversus length) was observed in myopic eyes compared to normal, whereas in the glaucomatous eyes, with or without myopia, no increase in anisotropy ratio was observed. Increasing volume of eyes can be caused by myopia and glaucoma. Myopic eyes were ellipsoid in shape, but there was less anisotropy and a near-spherical shape in glaucomatous eyes, even in glaucomatous myopic eyes.