This article is a critical review of the reasons for persistent and emerging post‐treatment endodontic disease (PTED). While there is a strong consensus that micro‐organisms, mainly bacteria, are practically the only cause of primary apical periodontitis, the reasons for persistent apical periodontitis lesions have been more a matter of debate. The authors of this review focus on the role of micro‐organisms in PTED, and while secondary developments such as cholesterol crystals or foreign material in the periapical area of a tooth with apical periodontitis may contribute to additional irritation and/or an inflammatory reaction, a detailed analysis of the available data suggests that evidence supporting a primary role for such secondary factors without the continued presence of bacteria is lacking. Therefore, even in PTED, elimination of micro‐organisms residing within the tooth structure, root surface, or periapical tissues remains the goal of treatment and the key to long‐term success.