Aim: Smear layer removal from artificially prepared internal root resorption (IRR) cavities using the self-adjusting file (SAF) system with activated continuous irrigation or the ProTaper system (Dentsply Maillefer, Ballaigues, Switzerland) with conventional syringe/needle irrigation was compared. Materials and methods: Twenty-eight maxillary central incisors were selected, decoronated and 20 of them were randomizedly splited along the coronal plane into labial and lingual sections, and artificial IRR cavities were prepared in both walls. Tooth segments were rejoined and teeth were divided into two groups. Each group (n = 10) was prepared using the SAF or ProTaper system with 12-mL 5.25% NaOCl and 12-mL 17% EDTA. Root canals were prepared in six intact positive control teeth using the SAF or ProTaper system with 5.25% NaOCl and 17% EDTA. As negative controls, two intact teeth were prepared using NaOCl only. Roots were than split longitudinally from the rejoined segments and samples were evaluated under scanning electron microscopy using a five-point scoring system. Results: Most SAF (87%) and ProTaper (83%) samples (P > 0.05), had scores of 1 and 2 indicating clean canal walls for the IRR cavities. Conclusions: SAF with activated continuous irrigation and ProTaper with conventional syringe/needle irrigation both successfully removed the smear layer from artificially prepared IRR cavities