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Modern developments in instrument design and obturation techniques have grossly improved the efficeincy of conventional endodontic therapy. Nickel titanium rotary instruments allow the practitioner to prepare canals more quickly and predictably. However, apical preparations by such instruments fail to address the anatomical complexity of the root canal system. Morphologic studies consistently show that canals are mostly oval or irregular in shape; therefore, round preparations by instrumentation result in uninstrumented areas of the root canal system. This is of particular importance in the apical third and in cases of preexisting periapical pathology, where residual bacteria may reside and cause persistent infections. How beneficial are these new instrumentation and obturation techniques to the basic purpose of root canal therapy in eradicating bacteria? This article presents the shortcomings of current instrumentation and obturation techniques and offers possible solutions to improve the outcome of endodontic therapy.