Background: The electrophysiological properties of the brain and influence of parental bonding in childhood irritable bowel syndrome (IBS) are unclear. We hypothesized that children with chronic gastrointestinal (GI) symptoms like IBS may show exaggerated brainstem auditory evoked potential (BAEP) responses and receive more inadequate parental bonding. Methodology/Principal Findings: Children aged seven and their mothers (141 pairs) participated. BAEP was measured by summation of 1,000 waves of the electroencephalogram triggered by 75 dB click sounds. The mothers completed their Children's Somatization Inventory (CSI) and Parental Bonding Instrument (PBI). CSI results revealed 66 (42%) children without GI symptoms (controls) and 75 (58%) children with one or more GI symptoms (GI group). The III wave in the GI group (median 4.10 interquartile range [3.95-4.24] ms right, 4.04 [3.90-4.18] ms left) had a significantly shorter peak latency than controls (4.18 [4.06-4.34] ms right, p = 0.032, 4.13 [4.02-4.24] ms left, p = 0.018). The female GI group showed a significantly shorter peak latency of the III wave (4.00 [3.90-4.18] ms) than controls (4.18 [3.97-4.31] ms, p = 0.034) in the right side. BAEP in the male GI group did not significantly differ from that in controls. GI scores showed a significant correlation with the peak latency of the III wave in the left side (rho = -0.192, p = 0.025). The maternal care PBI scores in the GI group (29 <xref ref-type="bibr" rid="pone.0032913-Janssens1"></xref>-<xref ref-type="bibr" rid="pone.0032913-Stockard1"></xref>) were significantly lower than controls (31 [28.5-33], p = 0.010), while the maternal over-protection PBI scores were significantly higher in the GI group (16 <xref ref-type="bibr" rid="pone.0032913-Fature1"></xref>-<xref ref-type="bibr" rid="pone.0032913-Dickhaus1"></xref>) than controls (13 [10.5-16], p = 0.024). Multiple regression analysis in females also supported these findings. Conclusions: It is suggested that children with chronic GI symptoms have exaggerated brainstem responses to environmental stimuli and inadequate parental behaviors aggravate these symptoms.