BackgroundThere is still a lack of knowledge regarding the permeability and configuration of infected root dentin. The aim of this ex vivo study was to compare the dentin penetrability of healthy teeth and necrotic teeth with apical periodontitis by evaluating the penetration of sodium hypochlorite (NaOCl) and to analyze the histopathological features of root dentin.MethodsForty-eight molars were collected and divided into two groups. The clinical diagnosis for one group was pulp necrosis with apical periodontitis and the pulp and periapex were normal in the other group. Forty-eight straight roots were divided into two groups: infected and healthy. First, all root canals were stained with 2% methylene blue to visualize penetration after standard root canal instrumentation and irrigation. Transverse sections were obtained, and the dye penetration parameters were measured. The cross sections were processed to 20–30 μm and stained with hematoxylin and eosin for observation of the histopathological changes in the root dentin.ResultsThe maximum penetration depth, median penetration depth and penetration percentage of NaOCl solutions, in infected root canals were significantly lower than those in healthy root canals. The histopathological analysis showed that the frequency of reparative dentin formation in infected root canals was significantly greater than that in healthy root canals.ConclusionsThe dentin penetrability of teeth with necrotic teeth and apical periodontitis was more superficial during root canal irrigation than that of healthy teeth. The histopathological changes in infected radicular dentin, namely the formation of reparative dentin, might be associated with the lower permeability of dentin tubules in human teeth with apical periodontitis.