BACKGROUND: Alteration in autonomic function has been implicated as a possible pathophysiologic mechanism in functional dyspepsia (FD) in adults.nnMETHODS: This was a two-part study. For the first part of the study, nine children with FD and 28 controls underwent heart rate variability (HRV) analysis for 30 min baseline and for 60 min following a test meal. For the second part of the study, eight children with FD and 26 controls underwent HRV analysis for 30 min baseline and for 60 min following rapid water loading. HRV analysis yielded measures for power in the high frequency (HF) band (vagal activity), power in the low frequency (LF) band (mainly sympathetic activity), and LF/HF (sympathovagal balance).nnRESULTS: HRV parameters did not differ between FD patients and controls in either baseline period or following water loading. Following the meal, HF was higher and LF and LF/HF were lower in FD patients as compared to controls. Baseline LF/HF was positively correlated with the water load volume in controls and negatively correlated with the water load volume in FD patients.