A new radiographic technique was used to compare apical transportation in four Ni-Ti rotary instrumentation sequences. Mesiobuccal canals of 60 extracted mandibular molars were randomly divided into four groups. Groups 1 and 3 were instrumented by crown-down and groups 2 and 4 by step-back technique with 0.06 ProFiles series 29 to size 6. In groups 3 and 4 Greater Taper files were first used in a crown-down manner. The central axes of initial and final instruments were radiographically superimposed to measure loss of working length (WL) and transportation at 0, 0.5, 1, 3, and 5 mm from WL. ANOVA test showed no significant differences among groups regarding degree of transportation or loss of WL. Transportation was negatively correlated with radius of curvature at 0.5 and 5 mm from WL. The results indicate that the operational sequence of ProFiles or preinstrumentation with GT files has no effect on degree of transportation and loss of WL.