Aim Apical extrusion of debris in primary root canal treatment has not been well elucidated. The purpose of this study is to compare the amount of apically extruded debris during the preparation of primary molar root canals using ProTaper, ProTaper Next, Selfadjusting File (SAF) and hand files. Methods One hundred sixty extracted primary mandibular molar teeth were assigned to 2 groups: Group 1: Resorbed (n=80) and Group 2: Nonresorbed (n=80) and randomly to four subgroups (n=20 teeth for each subgroup) according to the instruments used, ProTaper, ProTaper Next, SAF, and hand file. The apically extruded debris was collected and dried in preweighed Eppendof tubes. The dry weight was calculated by subtracting the preoperative weight from the postoperative weight. Statistics: Data were analysed statistically using the ANOVA and the Bonferroni post hoc t-test. Results The amount of apically extruded debris was significantly less for the non-resorbed group compared to the resorbed group (P<0.05). Regardless of the resorption groups, ProTaper Next and SAF extruded significantly less debris than did the ProTaper and hand files (P<0.05), while no statistically significant difference was found between ProTaper Next and SAF (P>0.05). Conclusion All instruments caused apically extruded debris in primary teeth.