Background Current endoscopic therapy for neoplastic Barrett’s oesophagus (BO) consists of complete resection/ablation of all Barrett’s tissue including neoplastic lesions. Recurrence seems to be frequent after thermal therapy, such as radiofrequency ablation. Objective To analyse long-term recurrence of neoplasia and BO after successful widespread endoscopic mucosal resection (EMR). Design In a retrospective analysis, all patients undergoing widespread EMR of neoplastic BO between 2002 and 2007 at two referral centres were followed for at least 3 years after completion of endotherapy. Recurrence was diagnosed if neoplasia and/or BO were detected following previous successful complete removal, defined as at least two negative endoscopies and biopsies. Results Ninety patients undergoing widespread EMR were included (mean age 63 years; 82 male), 58% of whom underwent additional thermal ablation for minor residual disease. Complete eradication of neoplasia and Barrett’s tissue was achieved in 90% of patients. On further follow-up (mean 64.8 months), recurrence of neoplastic and non-neoplastic BO was found in 6.2% and 39.5%, respectively. Recurring neoplasia (3 adenocarcinomas, 1 low-grade and 1 high-grade dysplasia) were found after a median of 44 months (range 38–85) and could be retreated endoscopically. In a multivariate analysis, Barrett’s length was the only factor significantly associated with recurrence (OR 2.73). Conclusions Even after seemingly complete endoscopic resection, recurrence of BO is frequent and independent of additional thermal therapy. Due to the possibility of neoplasia recurrence even after long disease-free intervals, follow-up should be extended beyond 5 years.