It is a well-established fact that bacterial infection of the dental pulp ultimately results in the formation of apical periodontitis. And apical periodontitis may develop periapical leisons consisting granulomas and cysts. In this article, we show the pathologic condition of infected root canal systems and periapical lesions immunohistologically. We also describe the possible causes of refractory apical periodontitis that conventional root canal therapy could not work effectively. Finally,we explain our newly developing treatment for refractory apical periodontitis named electro-magnetic apical treatment, and illustrate clinical efficacy of this treatment.