Monitoring metabolic adaptation to type 1 diabetes mellitus in children is challenging. Analysis of volatile organic compounds (VOCs) in exhaled breath is non-invasive and appears as a promising tool. However, data on breath VOC profiles in pediatric patients are limited. We conducted a cross-sectional study and applied quantitative analysis of exhaled VOCs in children suffering from type 1 diabetes mellitus (T1DM) (n = 53) and healthy controls (n = 60). Both groups were matched for sex and age. For breath gas analysis, a very sensitive direct mass spectrometric technique (PTR-TOF) was applied. The duration of disease, the mode of insulin application (continuous subcutaneous insulin infusion vs. multiple daily insulin injection) and long-term metabolic control were considered as classifiers in patients. The concentration of exhaled VOCs differed between T1DM patients and healthy children. In particular, T1DM patients exhaled significantly higher amounts of ethanol, isopropanol, dimethylsulfid, isoprene and pentanal compared to healthy controls (171, 1223, 19.6, 112 and 13.5 ppbV vs. 82.4, 784, 11.3, 49.6, and 5.30 ppbV). The most remarkable differences in concentrations were found in patients with poor metabolic control, i.e. those with a mean HbA1c above 8%. In conclusion, non-invasive breath testing may support the discovery of basic metabolic mechanisms and adaptation early in the progress of T1DM.