Obesity in children and adolescents has become an increasing clinical and public health concern (Semiz et al., 2007; Windham et al., 2012). Its prevalence has increased significantly worldwide with an alarming rise of its co-morbidities that elevate the cardiovascular risk of affected people. Obesity has been found to cause changes in cardiac autonomic modulation and was found to be associated with decreased heart rate variability (HRV) in adults. Analysis of HRV provides a non-invasive method for investigating the autonomic input to the heart. It quantifies the amount by which the RR interval or heart rate changes from one cardiac cycle to the next. It is a reliable reflection of many physiological factors modulating the normal rhythm of the heart, including the interplay between the sympathetic and parasympathetic nervous systems. However, the data on cardiac autonomic function in obese children is scarce and contradicting. Heart rate variability was found to be associated with risk factors in diabetic and non-diabetic subjects, namely higher glycosylated hemoglobin (HbA1c), serum triglycerides, systolic blood pressure, body mass index (BMI), and albumin excretion rate. Moreover, HRV in the severely obese was found to be better predicted by the degree of insulin resistance than by the degree of obesity, age, or gender.