Endodontic infection refers to the infection of the root canal system and is the major etiologic agent of apical periodontitis. Colonization of micro-organisms in the dental pulp and their movement into the periapical tissues has long been known as the main etiologic factor in pulpal inflammation. Bacteria are virtually always present and are regarded as the major microorganisms implicated in the pathogenesis of apical periodontitis. The cardinal principle of any healthcare profession is the thorough understanding of the disease etiology and pathogenesis, which provides a framework for effective treatment. In this context, understanding the microbiologic aspects of both pulpal and periapical pathologies forms the basis for endodontic practice and should be managed with an evidence-based approach.