Background: Endoscopic radiofrequency ablation (RFA) is a rapidly evolving therapeutic modality for early flat esophageal squamous cell neoplasms (ESCNs). However, the in vivo tissue effects of RFA on the esophageal wall are uncertain., Methods: We prospectively enrolled eight patients with flat-type early ESCNs who were treated with balloon-based RFA. We evaluated the in vivo tissue effect on the esophagus using endoscopic ultrasound (EUS) and the histology of retrieved coagulum., Results: The mean tumor length was 6.1 cm, and six of the eight patients achieved a complete response after primary RFA. Real-time evaluation of the tissue effect showed that the mucosa and submucosal layer were more edematous and thicker after RFA than before the procedure (mean 4.89 vs. 2.04 mm, p <.001), suggesting that the thermal effect of RFA may injure the submucosa. Histological evaluation of retrieved coagulum showed a severe cauterization (burning) effect with extensive cell necrosis; however, four cases had some residual viable neoplastic cells. Even though there were viable cells in the sloughed coagulum, half of the patients still achieved complete remission after RFA., Conclusions: Our findings suggest that the thermal effect of RFA may injure the submucosal layer and enable neoplastic epithelium to slough off without "burning."