Difficulty in the diagnosis of the endo-perio lesions complicates their management. Thorough history and careful clinical and radiographic examination are required to identify and accurately assess the contribution of each lesion to patient's problem, which in turn will determine the sequence that produces optimal results.The tooth anatomy and the etiology of endodontic-periodontal lesions offer a strong base for establishing a correct diagnosis. Due to the complexity of these affections, an interdisciplinary approach with a good collaboration between endodontists, periodontologists and microbiologists, is recommended.