Patients with eosinophilic esophagitis (EoE) require frequent evaluation of mucosal inflammation via endoscopy. Instead of endoscopy, mucosal evaluation in adults with esophageal cancer and candidiasis is achieved using a cytology brush inserted through a nasogastric tube (NGT). We conducted a prospective cross-sectional study in children and young adults scheduled for routine esophagogastroduodenoscopy (EGD) where in Phase 1, we performed esophageal brushing through the endoscope under direct visualization and in Phase 2, we inserted the brush through a Cortrak® NGT prior to endoscopy. Eosinophil-derived neurotoxin (EDN) measured by ELISA in the samples extracted from brushes was validated as the sensitive biomarker. We collected 209 esophageal brushing samples from 94 patients and we found that EDN in brushing samples collected via EGD or NGT was significantly higher in patients having active EoE (n = 81, mean EDN 381 mcg/mL) compared with patients having gastroesophageal reflux disease (n = 31, mean EDN 1.9 mcg/mL, P = 0.003), EoE in remission (n = 47, mean EDN 3.7 mcg/mL, P = 0.003), or no disease (n = 50, mean EDN 1.1 mcg/mL, P = 0.003). EDN at a concentration of ≥10 mcg/mL of brushing sample was found to accurately detect active EoE. NGT brushing did not cause any significant adverse effects. We concluded that blind esophageal brushing using an NGT is a fast, less invasive, safe, and well-tolerated technique compared with EGD to detect and monitor EoE inflammation using EDN as the sensitive biomarker.