Heart rate variability (HRV) analyses can provide a non-invasive evaluation of cardiac autonomic activity. How autonomic control normally develops in childhood and how this is affected by obesity remain incompletely understood. In this review we examine the evidence that childhood age and weight status influence autonomic control of the heart as assessed using HRV. Electronic databases (Pubmed, EMBASE and Cochrane Library) were searched for studies examining HRV in healthy children from birth to 18 years who adhered to the Task Force (1996) guidelines. Twenty-four studies met our inclusion criteria. Seven examined childhood age and HRV. A reduction in 24-hour LF:HF was reported from birth to infancy (1 year), while overall HRV (SDNN) showed a marked and progressive increase. From infancy to early-to-late childhood (from 12 months to 15 years) LF:HF ratio was reported to decline further albeit at a slower rate, while RMSSD and SDNN increased. Twenty studies examined the effects of weight status and body composition on HRV. In a majority of studies, obese children exhibited reductions in RMSSD (n = 8/13), pNN50% (n = 7/9) and HF power (n = 14/18), no difference was reported for LF (n = 10/18), while LF:HF ratio was elevated (n = 10/15). HRV changes during childhood are consistent with a marked and progressive increase in cardiac parasympathetic activity relative to sympathetic activity. Obesity disrupts the normal maturation of cardiac autonomic control.