OBJECTIVES: To characterize the determinants of heart rate variability (HRV) in youth with obesity across the glycemia spectrum. METHODS: A total of 94 adolescents, 15 +/- 2.1 years (21 with normal weight, 23 with overweight-normal glucose tolerance, 26 with prediabetes and 24 with type 2 diabetes [T2D]) underwent an assessment of body composition (dual-energy x-ray absorptiometry), 2-h oral glucose tolerance test with the calculation of indices of glycemia and insulin sensitivity (IS), inflammatory markers (high-sensitivity C-reactive protein [hs-CRP] and tumour necrosis factor-alpha [TNF-alpha]), and HRV by peripheral arterial tonometry. RESULTS: The HRV frequency-domain index (low-frequency to high-frequency ratio [LF/HF]), an estimate of the ratio between sympathetic and parasympathetic activity, increased across the glycemic spectrum, and was highest in T2D compared with the other three groups (p = 0.004). LF/HF correlated with %body fat (r = 0.22, p = 0.04); fasting (r = 0.39, p < 0.001), 2-h (r = 0.31, p = 0.004), and area under the curve glucose (r = 0.32, p = 0.003); hs-CRP (r = 0.33, p = 0.002) and TNF-alpha (r = 0.38, p = 0.006). In a linear regression model, fasting glucose (beta = 0.39, p = 0.003) and hs-CRP (beta = 0.21, p = 0.09) contributed to the variance in Ln LF/HF independent of IS, %body fat, age, sex, race-ethnicity and Tanner stage (R(2) = 0.23, p = 0.013). CONCLUSIONS: Youth with impaired glucose regulation have evidence of cardiac autonomic dysfunction with decreased HRV, and sympathetic overdrive (increased LF/HF). This dysfunction is mainly related to glycemia and systemic inflammation.