Objective To study the effect of the left bacteria on the root canal therapy.Methods 50 single-rooted teethwith chronic apical periodontitis were divided into two groups, one was instrumented with step-back technique and 2.5%NaOCl ultra- sonic irrigation for 3 min, then filled with Thermafil.Samples were taken after instrumentation to culture. The other was treated with traditional RCT at three visits.Results In 24 months the apical radiolucency were greatly reduced in all cases. There weren′t significant relationship among the postoperative pain and the left bacteria, the degree of the obturation or the pre-operative symptoms (P>0.05).Conclusion The effect of left bacteria in root canal filled with Thermafil wasn′t observed.