Background: The baseline impedance (BI) and the mean nocturnal baseline impedance (MNBI) serve as markers of mucosal integrity in patients with pathologic acid exposure time (AET). This work aims to investigate the association between the BI and MNBI with the AET in children. Methodology: A retrospective study was performed in children 18 years old with suspicion of gastroesophageal reflux disease who underwent both endoscopy and pH-impedance monitoring (pH-MII). Esophagitis was graded according to the Los Angeles classification. The pathological AET was determined depending on the age (!5% in patients >1 year and !10% in those ages 1 year). For the BI, 60 s measurements were taken every 4 h, and for the MNBI, 3 10 min measurements were taken between 1.00 and 3:00 AM; then, they were averaged. The means of BI and MNBI were compared with each other, with the AET, and other variables. Results: Sixty-eight patients were included, 25% of patients presented pathological AET. The mean of the MNBI was higher than BI in channels 6 (2195 vs 1997 V, P ¼ 0.011) and 5 (2393 vs 2228 V, P ¼ 0.013). BI and MNBI at channel 6 were lower in patients with pathological AET than in those with normal AET (1573 vs 2138 V, P ¼ 0.007) and (1592 vs 2396 V, P ¼ 0.004), respectively. Conclusions: Children with pathological AET had lower impedance values than those with normal AET. BI and MNBI measurements should be part of the routine MII-pH assessment in children.