The aim of this study was to evaluate the influence of different instruments and mechanisms of agitation of the irrigating solution on the penetration by confocal laser scanning microscopy (CLSM), and the bond strength (BS) of the filling material to the dentin by push-out test. Human premolars were distributed in two experimental groups (n=30), according to the instrumentation system: ProTaper Next (PN) or XP-endo Shaper (XS) and three irrigation protocol (n=10): NaviTip (Nv), XP-endo Finisher (XF), passive ultrasonic irrigation/ XP-endo Finisher (PUIXF). The 2.5% NaOCl and 17% EDTA were the irrigating solutions used. The filling was performed using a lateral condensation technique, with AH Plus added to 0.1% rodhamine B. The roots were sectioned, obtaining 2 slices for each third of the root. The first slice was submitted to the sealer penetration analysis and the push-out test. The second slice was submitted to qualitative analysis (SEM) of the union interface. For the penetration (%) Tukey showed that PNXF (82.38±13.48), PNPUIXF (82.48± 12.02), XSXF (82.24±11.28) and XSPUIXP (86.23±10.45) presented the highest values, different (p<0.05) from PNNv (68.29±15.12) and XSNv (71.41±16.50). The BS (MPa) test evidenced that in the cervical third, PNPF (4.92±1.04) and XPSPF (5.03±0.70) obtained the highest values differing from the others groups (p<0.05). CSLM and SEM showed greater penetration of the sealer on the entire length of the root canal when the irrigation solution was stirred. In conclusion that the association PUI and XP-endo Finisher favored the penetration and bond strength of the filling material to the root dentin.