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Objective The objective of this study was to identify the probable factors associated with pulpectomy failure of primary teeth through qualitative analysis by histopathology (HIST) and scanning electron microscopy (SEM). Study design A longitudinal clinical investigation of the efficacy of pulpectomy in primary teeth with irreversible pulp changes was carried out with 133 teeth (66 children) evaluated up to 48 months. The overall success was 86.1% during follow-up. Of the 18 teeth extracted as a result of treatment failure, 8 presented sufficiently undamaged roots to be randomly selected for HIST (n = 4) and SEM (n = 4) analysis. Results Necrotic tissue and chronic inflammatory cells were observed in all specimens submitted to HIST as external radicular resorption associated with Howship's lacunae. SEM analysis showed apical and furcation areas heavily infected with microorganisms and Howship's lacunae. Conclusion These findings suggest that the main factors responsible for pulpectomy failure were technique limitations associated with the morphological irregularities created by external/inflammatory resorption.