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Abstract Background High-risk human papillomaviruses (HPVs) are present and can cooperate with Epstein–Barr virus (EBV) to initiate and/or enhance the progression of several types of human carcinomas including cervical as well as head and neck; in parallel, it has been recently pointed out that these oncoviruses can be detected in human breast cancers. Thus, we herein explored the presence/co-presence of high-risk HPVs and EBV in breast cancer in Lebanese women. Methods A cohort of 102 breast cancer samples and 14 normal breast tissues were assessed for the presence of HPVs and EBV. Polymerase chain reaction (PCR) and immunohistochemistry (IHC) analysis in addition to tissue microarray (TMA) platform were used in this study. Results We found the presence of HPV in 66/102 (65%) of our samples, while EBV is present in 41/102 (40%) of the cohort. Additionally, our data showed that high-risk HPV types (52, 35, 58, 45, 16 and 51) are the most frequent in breast cancer in Lebanese women. Meanwhile, we report that high-risk HPVs and EBV are co-present in 30/102 (29%) of the samples; more significantly, our results indicate that their co-presence is associated with tumor grade (p = 0.03). Conclusion Our data revealed that HPVs and EBV are present/co-present in human breast cancer where they may play an important role in its development and/or progression; thus, we believe that further investigations are essential to confirm and elucidate the presence/co-presence of these oncoviruses and the underlying mechanisms of their interaction in breast carcinogenesis.