Apical lesions are diseases of infectious origin that can cause destruction of the surrounding periapical tissue, including bone tissue and periodontal ligaments, resulting in the loss of the affected teeth. Currently, the microorganisms present in pulp and apical disease are mostly studied as bacteria. However, in recent years, interest has been aroused in the study of viruses that could be present in apical lesions, and how these could affect the progression of disease. In the present study, we conducted a systematic review of the literature to evaluate and synthesize the scientific evidence on the presence of viruses and their possible role in pulpal and apical disease. This systematic review was performed according to the PRISMA reporting guidelines. The search for studies was performed in the PubMed and Web of Science databases. A total of seven studies published in the last 10 years were included. The types of samples used for virus analysis varied from one study to another. In all the included studies, the presence of any of the types of viruses studied was found, either in pulp or apical tissue. Herpesviridae family, Epstein-Barr virus (EBV) and Human cytomegalovirus (HCMV) stood out as the most commonly present in apical lesions. Further studies are required to clarify and understand the pathogenic role of viruses in pulpal and periapical disease.