The objective of this research was to evaluate, by scanning electron microscopy, the apical structure of extracted human permanent teeth with different degrees of pulp and periapical pathology. A total of 25 teeth were extracted: 5 teeth with vital pulp (group I); 10 teeth with pulp necrosis without radiographically visible periapical lesion (group II); 10 teeth with pulp necrosis with radiographically visible periapical lesion (group III). The root apex was sectioned and processed for scanning electron microscopy. In groups I and II, fibers covered the root cementum and there was no cementum resorption or microorganisms. There were areas of cementum resorption in group III with microorganisms on the root apex surface (biofilm) and no fibers. The authors conclude that the presence of chronic periapical lesions causes severe changes in the apical structure with a destruction of fibers and different degrees of cementum resorption forming lacunae in which bacterial biofilm persisted.