OBJECTIVE: This study investigated the influence of the last apical instrument of the ProTaper system with and without 2.5% sodium hypochlorite for cleaning mandibular central incisors. MATERIAL AND METHODS: Thirty two mandibular central incisors were divided into six study groups: Group I - F1 instrument with 2.5% sodium hypochlorite; Group II - F1 and F2 with 2.5% sodium hypochlorite; Group III - F1, F2 and F3 with 2.5% sodium hypochlorite; Group IV - F1 with distilled water; Group V - F1 and F2 with distilled water; Group VI - F1, F2 and F3 with distilled water. The two remaining teeth comprised the negative control group. The specimens were prepared following the principles of the technique suggested by the manufacturer and then submitted to histological preparation and morphometric analysis. Data were analyzed statistically by the Kruskal Wallis test at 1% significance level. RESULTS: There was statistically significant difference (p<0.01) between all study groups, except between Groups I and VI. CONCLUSIONS: It was concluded that no technique allowed complete cleaning of the root canals. However, the technique of finishing preparation of the apical third with the F3 instrument with 2.5% sodium hypochlorite irrigation was the most effective.