This study investigated the quality of root-end filling in cases of periapical lesions persisting after endodontic surgery. Ten patients requiring extraction of an endodontically treated tooth were included. The root-ends of extracted teeth were examined by scanning electron microscopy. Defects at the interface between the root-end filling and cavity margin were classified as ideal, imperfect (some marginal disruption) or inadequate (continuous marginal disruption involving >30% of the interface). Four cases were scored as imperfect, and six were scored as inadequate. A defective apical seal could favour continuous leakage of surviving bacteria and their by-products from the infected root canal system to periapical tissues, thereby sustaining inflammation.