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The cleaning effectiveness of automated and manual root canal instrumentation was investigated with the aid of a scanning electron microscope. Hand instrumentation was performed with K-Flexofiles used in a reaming working motion and according to the step-back technique and with Hedstrom files used in a filing motion. Automated preparation was performed with the KaVo-Endo Flash device featuring torque-limited rotation using K-Flexofiles, as well as with the mechanical ProFile system using rotary nickel-titanium instruments. Twelve teeth each with either straight or curved root canals were instrumented to size 40. After cracking the roots longitudinally (n = 120), the amount of debris and smear layer were quantified on the basis of a numerical evaluation scale (1 through 5). Comparison of manual instrumentation with the automated KaVo-Endo Flash resulted in an equivalent degree of canal cleaning. Complete cleanliness was not achieved by any of the techniques and devices investigated. Best instrumentation results, especially in curved canals, were obtained with rotary ProFile instruments.