The cleaning capacity of rotary Ni-Ti instrumentation using Profile GT files, coupled with irrigation energised by ultrasound, was evaluated. Thirty-six human mandibular incisors were instrumented in vitro using the crown-down technique with the Profile GT system to 1 mm from the anatomical apex to a size 30.04 taper file. The instrumented teeth were then divided randomly into four groups where various final irrigations were used: Group I: 100 ml of 1% NaOCl with a Luer-Lok syringe (control group); Group II, Group III and Group IV: final irrigation with 100 ml of 1% NaOCl energised by ultrasound for 1, 3 and 5 min, respectively. After biomechanical preparation, the apical thirds of the roots were submitted to histological processing and examination. The specimens were analysed at 40x magnification and the images submitted to morphometric analysis with an integration grid. anova showed a statistically significant difference (P < 0.01) between the irrigation techniques. Group I (Luer-Lok syringe) showed the highest percentage of debris (35.81 +/- 4.49) and was statistically different from the other groups energised by ultrasound: Group II (27.28 +/- 4.49), Group III (24.39 +/- 5.72) and Group IV (18.46 +/- 5.25). It was concluded that rotary instrumentation using Ni-Ti files associated with final irrigation of 1% NaOCl energised by ultrasound leads to better debris removal from the apical third of mesio-distally flattened root canal.