The objective of this study was to evaluate the antibacterial effect and the ultrastructural alterations of diode laser with different wavelengths (808nm and 970nm) and its association with irrigating solutions (2.5% sodium hypochlorite and 2% chlorhexidine) in root dentin contaminated by a five days biofilm. Thirteen uniradicular teeth were sectioned into 100 dentin intraradicular blocks. Initially, the blocks were immersed for 5min in 17% EDTA and washed with distilled water for 5min, then samples were sterilized for 30min at 120°C. The dentin samples were inoculated with 0.1mL of E. faecalis suspension in 5mL BHI (Brain Heart Infusion) and incubated at 37°C for 5days. After contamination, the specimens were distributed into ten groups (n=10) according to surface treatment: GI - 5mL NaOCl 2.5%, GII - 5mL NaOCl 2.5%+808nm diode (0.1W for 20s), GIII - 5mL NaOCl 2.5%+970nm diode (0.5W for 4s), GIV - 808nm diode (0.1W for 20s), GV - 970nm diode (0.5W for 4s), GVI - CHX 2%, GVII - CHX 2%+808nm diode (0.1W for 20s), GVIII - CHX 2%+970nm diode (0.5W for 4s), GIX - positive control and GX - negative control. Bacterial growth was analyzed by turbidity and optical density of the growth medium by spectrophotometry (nm). Then, the specimens were processed for analysis ultrastructural changes of the dentin surface by SEM. The data was subject to the One-way ANOVA test. GI (77.5±12.1), GII (72.5±12.2), GIII (68.7±8.7), GV (68.3±8.7), GVI (62.0±5.5) and GVII (67.5±3.3) were statistically similar and statistically different from GIV (58.8±25.0), GVIII (59.2±4.0) and control groups (p<0.05). SEM analysis showed a modified amorphous organic matrix layer with melted intertubular dentin when dentin samples were irradiated with 970nm diode laser; erosion of the intertubular dentin in blocks submitted to 808nm diode laser irradiation; and an increased erosion of the intertubular dentin when 2.5% NaOCl was associated to the different wavelengths lasers. All the therapeutic protocols were able to reduce the bacterial contingent in dentin blocks, and the association of diode laser and solutions did not significantly improve the reduction of the bacterial contingent.