This chapter reports on the possible complications that can be related to the procedures for filling the root canal system. It begins with a brief introduction and a description of the most common filling materials used in Endodontics, their characteristics and their history. The different obturation techniques used to fill the root canals in three dimensions will be also described to better understand possible complications due to technical problems. Difficulties arising while using the various obturation techniques will be extensively described, including the descriptions of the complications due to the obturation procedures, their prevention and their management. The possible consequences of the extrusion of filling materials over the apex will be described, giving particular attention to the description of the anatomical areas that may be possibly involved. Complications due to the chemical effect, the heat, and the mechanical damage will also be described and discussed.