Despite the introduction of hypoglycemic drugs, diabetes and related complications continue being a major medical problem. Diabetes long-term complications are not only related to the genesis of free radicals due to oxidation of glucose and to the non-enzymatic and progressive glycation of proteins but also to the endothelial dysfunction secondary to persistent hyperglycemia that causes cardiovascular complications. In an experimental model of streptozotocin (STZ) diabetic rats, the effect of five doses of an extract containing both an antioxidant (Rosmarinus officinalis) and folic acid were intragastrically administrated. Urine fingerprints of control and diabetic rats, both with and without treatment, were obtained by capillary electrophoresis with mass spectrometry (CE-TOF-MS). In order to have further biochemical knowledge of the effect, after treatment, rats were killed and plasma glucose, triglycerides, cholesterol, total protein, urea were analysed. Vitamin E in plasma and liver was also measured. Among the changes observed, the reduction in diuresis and plasma triglycerides, together with reduction in 2-aminobutyric, leucine/isoleucine, and dimethylglycine have shown that a short term nutraceutical treatment was able to reduce some of the complications in the STZ diabetic rats. In addition, this CE-MS metabolomic approach has permitted to identify metabolites related to metabolism of arginine, histidine, lysine and glycine in urine that can help monitoring the efficiency of treatments against the deleterious effects of type 1 diabetes.