AIM To compare in vitro the cleanliness of root canal walls following automated or manual instrumentation. METHODOLOGY Thirty extracted human maxillary central incisors, maxillary and mandibular canines and premolars with single root canals were used in this study. The teeth were divided into two groups. In group 1 (20 teeth) automated canal preparation was performed using Anatomic Endodontic Technology (AET). In group 2 (10 teeth) manual instrumentation was performed with K-Flexofiles. Irrigation was performed using alternately 3.00% NaOCl and 18% EDTA, followed by rinsing with saline. The roots were split longitudinally into halves and the canals examined using a scanning electron microscope. The presence of debris and smear layer was recorded at coronal, middle and apical thirds of root canals using a four-step scoring scale. Mean scores for debris and smear layer were calculated and statistically analysed for significance (P<0.05) between and within groups, using the Mann-Whitney-Wilcoxon and Friedman nonparametric tests. RESULTS At coronal and middle thirds the root canals prepared with manual instrumentation had significantly less surface debris on the canal walls compared with canals prepared with AET (p<0.05). At apical third root canals prepared with manual instrumentation had significantly more debris compared with AET group. The amount of smear layer was greater in the apical than in the coronal and middle thirds of the root and significantly less amount was in the AET group (P<0.05). CONCLUSIONS Complete cleanliness was not achieved by any of the techniques and instruments investigated. It may be inferred that the choice between AET and hand instrumentation should be based on factors other than the amount of root canal debridement, which does not vary high significantly according to the instruments used.