Diabetes mellitus is a metabolic disorder primarily characterized by elevated blood glucose levels and by microvascular and macrovascular complications which increase the morbidity and mortality. The aim of this study was to assess whether in high risk patients with type 2 diabetes mellitus whose blood pressure and lipid levels are well controlled still exist risk factors for microvascular changes and target organ damage (nephropathy and retinopathy). In this case control retrospective study 326 patients (111 with nephropathy and/or retinopathy and 215 controls) were enrolled. Nephropathy or retinopathy was present in 10.1% and 26.9% cases, respectively. Only 71% of patients (no significant difference between cases and controls) were treated with antidiabetic drugs. Therefore their diabetes was not properly controlled (hemoglobin A1c was 7.96% in cases and 7.58% in controls). Patients with microvascular changes had significantly longer diabetes than the controls (p < 0.05) but there were no significant differences between these two groups concerning lipids concentrations. Statins and fibrates were used by significantly less (p < 0.05) patients with microvascular complications than by those without them (21.6% vs. 36.3% and 1.8% vs. 17.2% respectively). The results of this study suggest that the duration of the disease and adequate control of glycaemia in patients with type 2 diabetes mellitus are more important for microvascular complications than the serum lipoproteins levels. Lipid-lowering treatment might have an impact on microvascular complications in patients with type 2 diabetes, irrespectively of their serum lipid levels.