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Purpose: The purposes of this study were (1) to assess the endotoxin levels in root canals of primary teeth with necrotic pulps and periapical lesions; and (2) to evaluate the correlation of endotoxin levels with the periapical lesion size. Methods: Twenty primary molars with necrotic pulps and periapical lesions were selected. Standardized radiographs were obtained and the lesions were measured. Material from each root canal was collected to quantify the bacterial endotoxin. The results were analyzed using Pearson's correlation, student's t test, and Fisher's exact test (α equals five percent). Results: The initial amount of bacterial endotoxin in the root canals ranged from 0.089 to greater than 50.00 endotoxin units (EU)/mL and was detected in 100 percent of the samples. A positive but not significant correlation was observed between the amount of endotoxin and periapical lesion size in primary molars. Conclusion: Endotoxin was observed in 100 percent of root canals of primary teeth with a periapical lesion. However, there was no statistical significance between bacterial endotoxin levels and the periapical lesion area. [ABSTRACT FROM AUTHOR]