Background: Gestational diabetes mellitus (GDM) is currently the most common medical complication in pregnancy, affecting approximately 13 % of all pregnant women. Although long-term effects on the offspring are still unclear, previous studies indicate ventricular myocardial changes. Objectives: The aim of our study was to investigate whether early biomarkers such as QT interval variability (QTV) are sensitive enough to predict these structural changes in children of GDM mothers. Methods: We focused on children of GDM mothers. Healthy children of mothers without GDM served as controls. All of them were examined at the German Heart Center, Munich, Germany. Heart rate variability (HRV) and QTV measures were extracted from 10 to 15 min Einthoven II electrocardiograms, split into 5 min windows, to characterize the effects of possible autonomic nervous system alterations and cellular ventricular mutations. Results: 75 children were included in this prospective observational case-control study; 42 of them were children of GDM mothers. The median age at the examination was 12 months (11–13 months). We found decreased QTV as a measure of ventricular repolarization variability in one-year-olds of GDM mothers compared to healthy controls (p < 0.05). Conclusion: We have found increased very low frequency HRV in females and decreased QTV in male children of GDM mothers, which suggests diverse responses and could reflect increased sympathetic tone and altered ventricular myocardium at a cellular level, respectively. Further work is required to understand the long-term significance of these findings in terms of providing an easy-to-use and cost-effective technology for early diagnosis of myocardial damage.