Background Gastroesophageal reflux disease (GERD) and esophageal dysmotility are common in patients with esophageal atresia (EA). The aim of this study was to evaluate GERD and esophageal motility patterns in children with EA using combined multichannel intraluminal impedance and pH (MII-pH) monitoring and high-resolution esophageal manometry (HREM), respectively. The reflux patterns seen in EA patients were also compared with a control group of normal children with suspected GERD. Methods A retrospective chart review was done on 35 patients with EA and 35 age- and sex-matched normal controls with suspected GERD, who had undergone 24-hour MII-pH monitoring. Impedance data were compared between both cohorts. Eight of the EA patients also underwent HREM. Results In the EA cohort, the median age was 53 months, with 21 males, and 71.4% had Type C EA. A total of 85.7% of the EA cohort and 40% of the control group were on proton-pump inhibitor (PPI) therapy during the MII-pH study. There was no significant difference in the total retrograde bolus movements (RBMs) between the EA cohort (1,457) and the control group (1,482). Acidic RBMs was significantly lower in the EA group (208) compared with the control group (689), p = 0.0008. Nonacid reflux index (NARI) was significantly higher in EA children (1.1; 0.0-7.8) compared with controls (0.6; 0.0-5.7), p = 0.0046. In EA patients, only 335/1,183 (28%) total symptom occurrences were associated with RBM. The mean distal baseline impedance (DBI) was significantly lower in EA (1,029.6 [410.9 SD] Ω) compared with controls (2,998.2 [1028.8 SD] Ω) with suspected GERD, p < 0.0001. By logistic regression, only PPI use had a significant effect on DBI, p < 0.0001. HREM was abnormal in all eight EA patients. Four out of eight EA patients had a different peristaltic pattern for their solid swallows compared with their liquid swallows in HREM. Conclusions MII-pH testing allowed increased detection of nonacid reflux events in EA patients, which would have been missed with standard pH monitoring alone. NARI was the only reflux parameter which was significantly higher in the EA cohort compared with the control group with suspected GERD. Majority (72%) of symptoms in EA patients were not temporally related to RBM in MII-pH testing. DBI was significantly lower in EA patients compared with controls. Esophageal motility by HREM was abnormal in all EA patients.