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Aim: To evaluate the 6‐year outcome of root canal treatment irrigated with 0.5% or 3% sodium hypochlorite (NaOCl). Methodology: The baseline trial was designed as a quasi‐randomized clinical trial. Patients referred for root canal treatment to an endodontic specialist clinic were recruited to the study (n = 298). The concentration of NaOCl was allocated quasi‐randomized to 271 subjects (0.5% [n = 139], 3% [n = 132]). Bacterial sampling was performed immediately before root canal filling. Samples were cultured and evaluated as growth or no growth. Patients were invited to a clinical and radiological follow‐up >5 years postoperatively. The clinical outcome measurements were tooth survival, cumulative incidence of endodontic retreatments, patients' assessment of pain, clinical findings and radiological signs of apical periodontitis (AP). Results: Tooth survival was 85.6% in the 0.5% NaOCl group and 81.1% in the 3% NaOCl group (p =.45). There was no record of retreatment in 94.4% in the 0.5% NaOCl group and in 92.2% in the 3% NaOCl group (p =.76). The percentage of asymptomatic cases were 87.8% in the 0.5% group and 85.3% in the 3% NaOCl group (p =.81). Absence of clinical signs of AP was seen in 86.6% in the 0.5% NaOCl group and in 83.6% in the 3% NaOCl group (p =.80). Absence of radiological signs of AP was seen in 74.0% in the 0.5% NaOCl group and 64.1% in the 3% NaOCl group (p =.20). Subjects with positive culture before root filling reported subjective pain with a significantly higher frequency as compared to negative‐culture subjects (p =.014). Conclusions: The use of 0.5% or 3% NaOCl for irrigation during root canal treatment resulted in similar clinical outcomes 5–7 years postoperatively. Persisting bacteria immediately before root filling may predict future episodes of subjective pain. [ABSTRACT FROM AUTHOR]