The aim of this study was to compare apical centring ability of nickel titanium (NiTi) ProTaper, RaCe and mainly stainless steel Safesider systems using micro-computed tomography. Thirty freshly extracted mandibular molars with two separate mesial canals and separate foramina were used for the study. Mesial roots were embedded in acrylic resin and instrumented with the ProTaper, RaCe or Safesider systems. Root canal transportation and centring ability of the instruments were evaluated using superimposed micro-computed tomography images of the apical 4mm of the roots taken at 1mm intervals. One-way analysis of variance and post hoc Tukey's tests were performed to compare apical transportations. Significant differences were observed between groups at the apical 1, 2 and 3mm levels (P<0.05). The reciprocating Safesider system transported root canals significantly more than the other two NiTi systems in the apical 1mm level (P=0.001) and more than RaCe system in the apical 2mm level (P=0.003). The ProTaper instruments caused more apical root canal transportation than did RaCe instruments at apical 3mm (P=0.045). NiTi instrumentation systems showed better centring ability than the mainly stainless steel Safesider system because of the flexible structure of the NiTi alloy.