Microbial biofilms are the chief therapeutic targets in the treatment of endodontic disease. Root canal instrumentation and chemicals facilitates root canal disinfection besides providing space for the conventional root-filling materials. Currently there are many file systems in the market and different philosophies being instructed for root canal instrumentation. However, recent years have witnessed a rising trend in the application of minimally invasive concepts in root canal treatment. This lecture will provide a scientific understanding on the effect of root canal instrumentation on the biomechanical effects of tooth in function. Changing concepts in root canal disinfection and root-filling that would be the foundation for biologically based root canal treatment in the near future will be also be discussed.