We isolated spore-forming gram-positive aerobic rods from three patients with persistent periapical periodontitis. These cells possessed unique phenotypic characteristics by exhibiting dense meshwork-like structures on their cell surfaces that could be found in a number of biofilm-forming bacteria. We identified these strains as Bacillus subtilis by the API system and 16S ribosomal RNA gene (rRNA) sequencing. Treatment of the meshwork-like structures with protease K and staining with calcofluor for polysaccharides indicated that these structures were polysaccharides in nature and could be essential for biofilm formation by these isolates. Our findings suggest that B. subtilis could form biofilms in periapical periodontitis lesions, and this might contribute to the resistance to treatment resulting in the development of persistent periapical periodontitis observed in these patients. The particular mechanisms for B. subtilis biofilms to develop periapical periodontitis are still unknown. Further studies are needed to clarify the role of biofilms in persistent infections.