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Objective To analyze autonomic functioning which presented as the high frequency ( HF) component of heart rate variability, a measurement of vagal tone, and the ratio of low frequency ( LF) to HF (LF : HF), an indicator of sympathovagal balance in irritable bowel syndrome ( IBS) patients. Methods We identified relevant studies by performing a literature search of MEDLINE, EMBASE and the ISI Web of Knowledge to 31 March 2013. Pooled effect sizes with 95% confidence interval ( CI) were calculated using a random effects model. Between-study heterogeneity was assessed using the Q test and I2 statistic. Results In all, 11 articles including 392 IBS patients and 263 controls met the inclusion criteria of the analysis. IBS patients had lower HF band power ( Hedges's g = −0.38, 95% CI −0.68 to −0.09) than the controls ( I2 = 63.6%, P = 0.003). Moreover, IBS patients showed a higher LF : HF ( Hedges's g = 0.43, 95% CI 0.13-0.74), with no significant heterogeneity. A subgroup analysis of the HF index according to the recording time yielded different results for the IBS patients and controls. Additionally, constipation-predominant IBS ( IBS- C) patients had decreased HF band power, whereas no significant difference was found in LF : HF. Conclusions Impaired parasympathetic functioning and abnormal sympathovagal balance may be involved in the pathogenesis of IBS. Vagal dysfunction is more obvious in the IBS- C subgroup. [ABSTRACT FROM AUTHOR]