The aim of this randomized clinical trial is to compare the antibacterial effects of 1% sodium hypochlorite (NaOCl) and 2% chlorhexidine gluconate (CHX) during retreatment of teeth with apical periodontitis (AP).

Root canal-treated teeth with AP were randomly distributed in two groups according to the irrigant used. After removal of the previous filling material, bacteriological samples were taken from the canals before (S1) and after chemomechanical preparation using either NaOCl or CHX (S2), and after calcium hydroxide medication for 2-3 weeks (S3). 16S rRNA gene-based real-time qPCR was performed to detect and quantify total bacteria, Streptococcus species and Enterococcus faecalis.

Inclusion Criteria:

• Clinical diagnosis of apical periodontitis in a root-filled tooth assessed by radiography.

Exclusion Criteria:

• Presence of gross carious lesions in the diagnosed tooth,
• Presence of fractures involving the periodontium of the diagnosed tooth,
• Presence of periodontal pockets more than 4 mm deep in the diagnosed tooth,
• Diagnosis of diabetes,
• Diagnosis of HIV infection,
• Other immunocompromising disease,
• Antibiotic therapy within the previous 3 months.