BACKGROUND: Autonomic nervous system dysfunction and sympathetic nervous system over-activity play important roles in the development of hypertension associated with chronic kidney disease (CKD). In adults, increased blood pressure variability (BPV) appears to be directly related to sympathetic over-activity with increased risk of end-organ damage and cardiovascular events. Decreased heart rate variability (HRV) has been observed in adults with CKD, and is an independent predictor of mortality. METHODS: The purpose of this study was to evaluate BPV and HRV in pediatric patients enrolled in the Chronic Kidney Disease in Children Study. Ambulatory blood pressure monitoring data were available for analysis of 215 person-visits from 144 children that were not receiving antihypertensive medications. RESULTS: BPV and HRV were determined by standard deviation and coefficient of variation for heart rate and systolic and diastolic blood pressure for each patient averaged for wake/sleep periods during 24-h monitoring. Uniformly lower values were displayed during sleep versus wake periods: BPV was 20 % lower during sleep (p < 0.001) and HRV was 30 % lower during sleep (p < 0.001). A significant increase in systolic BPV was observed in hypertensive children compared to children with normal blood pressure (6.9 %, p = 0.009). Increased diastolic BPV was detected among hypertensive children during sleep period compared to children with normal blood pressure (11.5 %, p = 0.008). There was a significant decrease in HRV in hypertensive compared to normotensive children (-8.2 %, p = 0.006). CONCLUSIONS: These findings are similar to those in adult patients and may underscore childhood origin and natural progression of adverse cardiovascular outcomes in adults with CKD.