Tissue injury induced by intra‐canal procedures and substances extruded through the apical foramen may influence the development of post‐operative pain as well as the outcome of root canal treatment. While the development of pain is related to the intensity of tissue damage, treatment outcome is more dependent on the persistence of the source of injury. Procedural errors are the main causative agents of either post‐operative pain or persistent periradicular lesions. However, even when the treatment has followed the highest standards, post‐operative pain can occur and periradicular disease can persist, albeit at a lower incidence when compared to teeth treated to a poor technical standard. This paper critically reviews the effects of intra‐canal procedures on the periradicular tissues, with special emphasis on the occurrence of post‐operative pain and the outcome of the root canal treatment. The possible systemic effects stemming from root canal procedures are also discussed in the light of current knowledge.