Objective: The aim of this study was to investigate the presence of human cytomegalovirus (HCMV) and Epstein-Barr virus (EBV) in the tissue of chronic periapical lesions, and to compare the results in relation to the symptoms of patients and the size of the lesion. Methods: Periapical lesions analyzed in the study were collected from the roots of the teeth indicated for extraction. Samples were divided according to the symptoms into groups of symptomatic and asymptomatic, and according the size into groups of small and large lesions. Polymerase chain reaction was used to detect HCMV and EBV. The amplification was performed in a DNA Thermal Cycler (Hybaid). Results: Symptomatic lesions were 7.68 times more likely to be infected with HCMV than asymptomatic lesions (p < 0.001). Large symptomatic lesions were 73.50 times more likely to harbor HCMV than small symptomatic lesions (p < 0.001). Large symptomatic lesions were 7.64 times more likely to be infected with EBV than small symptomatic lesions (p = 0.05). Large symptomatic lesions were 5.38 times more likely to harbor dual HCMV/EBV infection than small symptomatic lesions (p = 0.115). Conclusion: Detection of HCMV and EBV in the samples of periapical lesions suggests an important role of herpesviruses in periapical tissue destruction.