Background: Oral mucosal lesions are more prevalent in diabetic patients compared to healthy individuals. Periodontal disorders have been known as the sixth complication of diabetes mellitus after microvascular and cardiovascular complications. The aim of this research was to assess the relationship between oral mucosal lesions and retinopathy and nephropathy in type 2 diabetic subjects in the Yazd province. Methods: This analytical cross-sectional study was conducted in diabetes research center during 2014-2016 in Yazd. Individuals with glomerular filtration rate (GFR) less than 60, oropharyngeal cancer, pregnancy, lactation, type one diabetes, or newly diagnosed diabetes (< 2 years) are excluded from study. The subjects' demographic data and oral examination was performed by an oral medicine specialist. Soft tissues oral cavity findings consist of any form of candidiasis, periodontitis, gingivitis, xerostomia, geographic tongue, lichen planus, gingival hyperplasia, delay oral wound healing, fissured tongue, and burning mouth sensation. Fasting blood sugar (FBS), HbA1c, and micro-albuminuria were checked. Diabetic nephropathy defined to the urinary excretion rate of albumin above 30 mg/g creatinine. The retinal specialist evaluated diabetic retinopathy. Finally, frequency of soft tissue oral lesions in individuals with and without retinopathy and nephropathy were compared. We analyzed data using the SPSS version 20. Statistical significance less than 0.05 were accepted. Results: Totally, 274 patients (48% male) participated in this study. Most of the patients (70.8%) suffer from at least one of the diabetic microvascular complications (retinopathy, nephropathy or both) and 80 diabetic patients (29.2%) had no complications. Gingivitis (P = 0.049) and fissured tongue (P = 0.047) were more prevalent in retinopathic individuals compared to subjects without retinopathy. Fissured tongue and delayed wound healing were high in nephropathic persons compared to other groups (P = 0.047 and 0.039, respectively). Presence of at least one of the oral lesions are higher than in patients with retinopathy and nephropathy compared to individuals without complications (P = 0.047 and 0.049 respectively). Conclusions: High frequency of oral problems in subjects with micro-vascular complications were found. Our findings showed that closer cooperation between the endocrinologist and the oral medicine specialist is required. In addition, diagnosis of oral problems in diabetics, especially with micro-vascular complications, is necessary to improve the oral health of them.