Background: A successful primary root canal treatment depends on effective shaping and cleaning the root canal system and finally filling it with a hermetic sealer. Clinically, roots of primary teeth are difficult to shape and the irrigation/disinfection protocol has great importance on prognosis. Objective: The present study evaluated the antibacterial efficiency of Endosafe (Orangedental GmbH & Co. KG), photo-activated disinfection (PAD; Orangedental GmbH & Co. KG), diode laser (Epic 10; Biolase, Inc.), ozone (O-3, Ozonytron; Biozonix, Munchen, Germany), and sodium hypochloride applications in primary root canals that were infected with Enterococcus faecalis after standard mechanical instrumentation. Methods: The study was conducted on roots of 100 human primary molar teeth, which were extracted due to excessive caries. The roots were divided in 5 groups with 15 roots in each root disinfection protocol. In addition, 15 samples and 10 samples served as positive and negative controls, respectively. The Shapiro-Wilk test, the Kruskal-Wallis test and then by post hoc group comparisons with the Bonferroni-adjusted Mann-Whitney U test (unpaired observations) was used. Results: Sodium hypochlorite (NaOCl) exhibited the highest antibacterial effect (0 colony-forming units per mL). Diode laser irradiation was statistically more effective than the ozone, PAD, and Endosafe groups (p<0.001). Endosafe, PAD, and ozone groups showed similar antibacterial effect (p>0.05). Although not statistically significant, the Endosafe was more effective in reducing the bacterial count when compared with ozone and PAD. Conclusions: The five tested irrigation systems were shown to be effective in disinfection of the E. faecalis-contaminated primary root canals and best results were obtained with 2.5% NaOCl and diode laser.