Coronal leakage has been considered as one of the major causes of failure in root canal treatment. Bacteria have been shown to penetrate the root canal obturating materials and influence the periapical tissues. Endotoxin, a component of Gram-negative bacteria, is a potent inflammatory agent and may be able to penetrate obturating materials faster than bacteria. This in vitro study examined the possible penetration of post-prepared canals by endotoxin and bacterial cells derived from mixed bacterial communities. Results showed that both bacteria and endotoxin were able to penetrate the obturating materials in post-prepared canals; however, endotoxin penetration was faster than bacterial. If one speculates that a similar sequence of events occurs clinically, then such a rapid penetration of endotoxin could lead to an early periapical reaction, with subsequent treatment failure and need for retreatment or periapical surgery. The need for an immediate and proper coronal restoration after root canal treatment is therefore reinforced.