Background The purpose of this study was to observe whether invisible morphological changes are presented in the two types of diabetes mellitus patients without diabetic retinopathy. Methods Twenty-six type 1 diabetes mellitus (T1DM) patients and 34 type 2 diabetes mellitus (T2DM) patients without diabetic retinopathy (DR) were recruited for this study. They underwent complete examinations that included stereoscopic color fundus photography and optical coherence tomography (OCT). The OCT patterns were used to measure the macular retinal thickness (RT), the ganglion cell and inner plexiform layer (GC-IPL) complex thickness, the inner nuclear layer (INL) thickness, the outer nuclear layer (ONL) thickness and the subfoveal choroidal thickness (SFCT) using the enhanced depth imaging (EDI) patterns and the retinal fiber layer (RNFL) thickness around the optic disc. All results were compared to those of age- and sex-matched control groups. Results In the patients with T1DM, the mean RT and GC-IPL complex thicknesses were significantly thinner than those of the control group (p