Objective: To assess debris and smear layer remaining following canal preparation with ProTaper hand-operated rotary instruments and stainless steel K-files. Methods: Sixty freshly extracted single-rooted mandibular premolars due to orthodontic treatment were randomly assigned to three groups of 20 premolars each. The canals were prepared by a rotary or manual ProTaper system using a crown-down technique, or by stainless steel K-files using a step-back technique. After each instrument, the root canals were flushed with 2 ml of a 5.25% NaOCl solution and at the end of instrumentation with 2 ml of a 5.25% NaOCl and 5 ml of distilled water. The amount of debris and smear layer were evaluated at the apical, middle and coronal regions by scanning electron microscopic photomicrographs and the data were analysed separately using Walloon's test. Results: In the coronal and middle thirds, both ProTaper groups achieved better results than the K-file group, and there was no significant difference between the two ProTaper groups. In the apical third, no significant difference for debris and smear layer was found among the three groups. Conclusion: Under the conditions of the present study, ProTaper hand-operated and rotary instruments resulted in relatively good cleaning in the coronal and middle thirds, but there was no difference among the three instruments in the apical third. Keywords: canal preparation, cleanliness, nickel-titanium (NiTi), scanning electron microscope (SEM)