Introduction: The ability of 2 different approaches to supplement the antimicrobial effects of chemomechanical debridement in infected root canals was compared in vivo. Methods: Samples from necrotic root canals of teeth with apical periodontitis were taken at the baseline (S1), after preparation with rotary nickel-titanium BioRaCe instruments and 2.5% NaOCl irrigation (S2), and then after either passive ultrasonic irrigation (PUI) for activation of NaOCl (n = 13) or a final rinse with 2% chlorhexidine (CHX) (n = 14) (S3). The incidence of positive culture for bacteria and fungi as well as positive broad-range polymerase chain reaction (PCR) results for bacteria, fungi, and archaea was determined. Results: All S1 samples were positive for bacteria in all methods. Fungi were not detected, and archaea occurred in only one S1 sample. Treatment procedures were significantly effective in reducing the incidence of positive culture and PCR results. Although both supplementary approaches reduced the incidence of positive bacteriologic results when compared with postinstrumentation samples, reduction was not statistically significant (P >.05). There was no significant difference for intergroup comparisons either (P > .05). Conclusions: Although supplementary disinfection with either PUI or a final rinse with CHX can reduce the number of cases with positive culture and PCR results for bacteria, many cases still remain with detectable bacteria in the main root canal. Research on alternative or supplementary antimicrobial methods or substances should be encouraged. Copyright © 2012 American Association of Endodontists.