OBJECTIVE: Measurements of heart rate variability (HRV) are increasingly used as markers of cardiac autonomic activity. The aim of this study was to investigate the characteristics of HRV in children with palpitations of unknown causes so as to provide a basis for the etiologic diagnosis of palpitations. METHODS: Thirty-four children with palpitations of unknowns causes (Study group) and 27 aged-matched healthy children (Control group) were enrolled in this study. Three time domain indexes of HRV from 24-hr Holter monitoring (SDNN, RMSSD and PNN50) were analyzed. The changes of ST-T segment and the circadian variation of heart rate were examined. RESULTS: Three time domain indexes of HRV significantly decreased in the Study group compared with those of the Control group (P <0.05). Fifteen patients in the Study group showed ST-T segment changes, characterized by a descended ST segment and a low-flat T wave during daytime but the changes disappeared during sleep. The circadian changes of heart rate were also observed in the 15 patients. The change characteristics were consistent with the diagnostic criteria of beta-receptor hypersensitivity. CONCLUSIONS: Three time domain indexes of HRV decrease in children with palpitations of unknown causes. HRV analysis along with ST-T segment change characteristics appears to be helpful for the etiologic diagnosis of this disease.