The aim of the present study was to characterize, by means of SEM, primary endodontic infections and to correlate with clinical and radiographic findings. Twelve (12) human extracted teeth (19 roots) presenting primary endodontic infection were examined. SEM qualitative observations of bacterial and defense cells, their features and distribution within the root canal lumen and root dentine were recorded for association with clinical and radiographic tabled data. Although a direct correlation between biofilm composition and clinical/radiographic findings was not established, structural organization and distribution of the biofilm, as well as the characteristics of host response, could be easily related to those features. Bacterial biofilm was predominant at the apical third. Symptomatic apical periodontitis was related to presence of bacterial biofilm all thirds. Defense cells could be seen in the apical third of some samples. These cells were present in all thirds in some of the cases with open cavities. The correlations performed in this study allowed a better understanding of the picture of primary endodontic infection, host response and relevant clinical features. The combined use of scanning electron microscopy with clinical and radiographic evaluation has the potential to overcome some limits of the current knowledge related to pulpal and periapical diseases, providing important insights for improving treatment strategies. Microsc. Res. Tech., 2012. © 2012 Wiley Periodicals, Inc.