The principal function of root filling materials is to prevent invasion of bacteria and infection of the root canal system after completed endodontic treatment. This is accomplished by the formation of a tight, permanent seal with the surrounding tooth structure, leaving no space for invasion of or colonization by bacteria. The materials can also have a direct antibacterial effect and kill the microbes when in contact with them. Materials applied onto larger areas of connective tissue, i.e. for retrograde root fillings or perforation repair, should also allow or stimulate complete repair or regeneration. Ideally, the selection of materials for various applications in endodontics should be based on clinical, scientifically valid data. However, most current endodontic practices and choice of materials are based on a convoluted history where data of varying relevance and validity is mixed with experts’ stated opinions and manufacturers’ advertising. In this review, the chemical, physical, and biological properties of different root filling materials are discussed together with their handling characteristics and recommended use in the clinic. Emphasis is placed on evidence generated from clinical practice and research.