The use of gutta-percha in dentistry and in particular root canal procedures has a long and tortuous history; its use has been the preferred obturation material of choice for well over a century, in spite of attempts to eliminate it for other entities that were erroneously perceived to be superior. However, because of the importance of asepsis and bacteriological control in the delivery of quality root canal procedures, the clinical disinfection of gutta-percha cones has arisen as a controversial issue as to its need and the use of the most effective agent for rapid chairside management. This review will touch upon a brief history of the material and subsequently delve into the issues surrounding the decontamination/disinfection of this material in the hope to establish the best evidence for the clinical choice of managing this challenge. Keywords: antibiotics, atomic force microscopy, chlorhexidine, culturing, decontamination, disinfection, glutaraldehyde, gutta-percha, NaOCl