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Objective-To determine whether endodontic infections could harbor common etiologic agents of respiratory infections such as Streptococcus pneumoniae and Chlamydia pneumoniae.Methods-Specimens were aseptically obtained from 40 patients with endodontic infections. For the detection of C. pneumoniae, a single step 16S rRNA based PCR and a nested PCR targeting aromatic amino acid hydroxylase were used. For the identification of S. pneumoniae, primers targeting 16S rRNA gene and autolysin (lytA) were used.Results-Of 21 patient samples tested with the 16S rRNA-based PCR for S. pneumoniae, positive amplification was observed in all except three specimens. However, sequencing and phylogenetic analysis revealed that the product belonged to other bacterial phylotypes. The lytA-based PCR for S. pneumoniae and both PCR assays for C. pneumoniae failed to detect these organisms in all the specimens tested.Conclusions-S. pneumoniae and C. pneumoniae were not present in endodontic infections. PCR primers with less stringent specificity will inaccurately identify respiratory pathogens.