There is a clinical dilemma about root canal preparation for endodontic treatment of primary teeth. This study aimed to compare the amount of dentin removal in root canal treated primary molar teeth with three preparation techniques by cone-beam computed tomography (CBCT). A total of 39s primary molar teeth were selected with a minimum of two-thirds of the entire root length. Access cavity was prepared and preliminary CBCT images were taken and viewed by Romexis programme. The wall thickness of the canal was measured in the danger zone at two axial cut sections of 1 and 2mm below furcation. Then, the teeth were instrumented with three different methods as manual K-files (size 15-30), Gates glidden burs (in decreasing order of size #2 and #1 followed by hand k-files up to file number 25), and ProTaper rotary files. After canal preparation, the specimens were placed in the same position, and the canal wall thickness was remeasured. Data were analysed by using one-way ANOVA and Kruskal-Wallis tests (α = 0.05). The amounts of removed dentin thickness was not significantly different among the three groups at two axial cut sections of 1mm and 2mm below furcation (P = 0.27 and 0.17, respectively). Within the limitations of this study, the three instrumentation techniques used in primary molars were comparable regarding the amount of dentin removal.