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Background: Endothelial dysfunction (ED) is a marker of vascular damage. Glycated hemoglobin (A1C) predicts vascular complications. The EndoPAT (peripheral arterial tonometry) device calculates the reactive hyperemic index (RHI), a measure of endothelial function. The greater the vasodilation, the higher the RHI. We hypothesized that children with poorly-controlled diabetes mellitus (DM) and non-diabetes mellitus (NDM) obese children have ED. Methods: A cross-sectional study using the EndoPAT device was performed on children with poorly-controlled DM and NDM children. ANOVA, t-test, Mann-Whitney U test, multiple linear regression and Spearman correlation were used. Results:Of 58 children that completed the study (aged 13.1 ± 3.42 years), 33 with type 1 diabetes (T1DM), 8 with type 2 diabetes (T2DM) and 17 were NDM obese children. Eighty-five percent were African-American, 60% were female and 79% entered puberty. The RHI of children with DM (1.42 ± 0.48) versus NDM obese group (1.40 ± 0.34) was not different (P = 0.86) regardless of the type of DM or body mass index. In the DM group, for every 1% increase in latest A1C, the RHI decreased by 0.097 (P = 0.01) after adjusting for age, gender, and type of DM. The RHI of DM patients with latest A1C of < 10% (1.70 ± 0.58) versus those with A1C ≥10% (1.21 ± 0.19) was statistically different (P = 0.02). In the total study population, males had significantly lower RHI (1.28 ± 0.36) when compared to females (1.51 ± 0.46), P = 0.04 but this difference disappeared when considering pubertal status and type of diabetes. Conclusions: Our data showed that patients with poorly-controlled DM as reflected by latest A1C of ≥ 10% had worse endothelial function as reflected by lower RHI score.