This study aimed to comparatively evaluate the disinfecting potential of sodium hypochlorite, diode laser, and photodynamic therapy in non-vital teeth with or without periapical rarefaction. Forty-five patients with the diagnosis of pulp necrosis with apical rarefaction were randomly assigned to three groups (n = 15) based on the disinfection protocol. Access cavities were prepared and pre-instrumentation microbial samples were taken using a paper point. Working length determination followed by cleaning and shaping with rotary files was performed. The canals were lubricated with ethylenediaminetetraacetic acid (EDTA) during instrumentation and finally rinsed with copious amounts of saline. Canals in group 1 were irrigated with 5 mL of 5.25% NaOCl, those in group 2 received irradiation with 808-nm diode laser (30 s, 7W), and those in group 3 were soaked with methylene blue photosensitizer (5 min) before irradiation with 660-nm diode laser (3 min). Post-disinfection microbial samples were collected using a paper point. Pre- and post-disinfection live bacterial counts were analyzed using a flow cytometer. The data were statistically analyzed using one-way ANOVA and Student's t-test. Comparison of pre-instrumentation mean live bacterial count showed no significant difference between the groups (p > 0.05). The mean live bacterial count post-disinfection was 41.07%, 46.99%, and 34.45% in groups 1-3 respectively. A significant reduction in the bacterial count was seen following disinfection in all the groups (p < 0.05). It can be concluded that both diode laser and photodynamic therapy were equally effective as 5.25% NaOCl in reducing the bioburden in root canals. TRIAL REGISTRATION: CTRI/2018/03/012667.

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