OBJECTIVES: Heart rate variability (HRV), a marker of the parasympathetic vagal activity, was reportedly significantly lower in patients with inflammatory bowel disease (IBD) compared to healthy controls. The aim of this study was to evaluate HRV as a predictor of clinical outcomes in pediatric IBD. METHODS: This was a prospective study. Children (12-18 years of age) with IBD were prospectively recruited. Each patient underwent two 10-min HRV measurements by means of a photoplethysmograph finger sensor. The square root of the mean squared differences of successive R-R pulse intervals (RMSSD), an indirect index of vagal activity, was calculated. Clinical data, including demographic variables, disease activity and course, medications, and laboratory results were collected during a follow-up of 12 months. The relation between RMSSD and clinical outcomes was examined, adjusting for confounders. RESULTS: A total of 34 children with IBD were included. Patients in clinical remission had a significantly higher RMSSD compared to patients with active disease (67.72 +/- 27.81 versus 45.76 +/- 22.04, respectively, P = 0.022). A multivariate analysis revealed that a higher RMSSD was a significant and independent predictor of lower risk of IBD exacerbation (odds ratio = 0.941, 95% confidence interval 0.887-0.998, p = 0.044). CONCLUSION: HRV correlates with IBD activity and may also serve as an independent predictor of disease exacerbation in pediatric IBD.