Emerging evidence suggests that diabetes mellitus (DM) is associated with iron and calcium metabolism. However, few studies have investigated the presence of DM in cognitively impaired patients and its effect on brain iron and calcium accumulation. Therefore, we assessed the effects of DM on cognitively impaired patients using quantitative susceptibility mapping (QSM). From June 2012 to Feb 2014, 92 eligible cognitively impaired patients underwent 3T magnetic resonance imaging (MRI). There were 46 patients with DM (DM+) and 46 aged matched patients without DM (DM-). QSM was obtained from gradient echo data and analyzed by drawing regions of interest around relevant anatomical structures. Clinical factors and vascular pathology were also evaluated. Measurement differences between DM+ and DM- patients were assessed by t tests. A multiple regression analysis was performed to identify independent predictors of magnetic susceptibility. DM+ patients showed lower susceptibility values, indicative of lower brain iron content, than DM- patients, which was significant in the hippocampus (4.80 ± 8.31 ppb versus 0.22 ± 10.60 ppb, p = 0.024) and pulvinar of the thalamus (36.30 ± 19.88 ppb versus 45.90 ± 20.02 ppb, p = 0.023). On multiple regression analysis, microbleed number was a predictor of susceptibility change in the hippocampus (F = 4.291, beta = 0.236, p = 0.042) and DM was a predictor of susceptibility change in the pulvinar of the thalamus (F = 4.900, beta = - 0.251, p = 0.030). In cognitively impaired patients, presence of DM was associated with lower susceptibility change in the pulvinar of the thalamus and hippocampus. This suggests that there may be region-specific alterations of calcium deposition in cognitively impaired subjects with DM.