The aim of this study was to investigate relation between level of HbAc1 and concentration of metabolites in urine of T1D patients. To test this hypothesis the 1H NMR (proton nuclear magnetic resonance) target analysis of crucial urine metabolites combined with chemometric approach were applied. Urine samples were collected from 30 children and teenagers aged 4–19 with T1D and 12 healthy children, aged 9, as control group. Patients were divided into two groups according to their level of glycated hemoglobin (HbA1c): below (L-T1D) and above 6.5% (H-T1D). The multivariate data analysis (OPLS-DA) was used to explore data and generate the models for selected groups of patients. Two tailed unpaired t-test was used for statistical analysis of quantified metabolites. Comparing to L-T1D patients, H-T1D group exhibited increased levels of alanine, pyruvate and branched amino acid valine that might be related with endogenous glucose production pathway from proteins as well as in the case of T2D. Application of 1H NMR spectroscopy together with target analysis and chemometric tools based on urine metabolite concentration enable to monitor T1D patients. This methodology can be used as supporting tool for marker HbA1c analysis providing comprehensive information about T1D progression and treatment efficiency.