Human papilloma viruses (HPV) may have a role in some breast cancers. General methods for screening for HPV include PCR on genomic DNA and RNA. Other methods include in situ PCR, CISH, ELISA and recently NGS, all of which have limitations. Immunohistochemistry screening of the HPV E7 oncogenic protein has the advantage of reduced time and cost. To validate this procedure, immunohistochemistry results were compared to a retrospective cohort study that used PCR to identify HPVs in archival specimens from 41 Australian women with benign breast biopsies who later developed breast cancer. PCR analysis revealed the presence of HPV sequences in both the benign and invasive carcinoma samples from the same patients (cc = 0.476, p = 0.003). In 14 patients, the same HPV type was present in both the benign breast and subsequent breast cancer. Immunohistochemistry to detect the HPV E7 protein on the same samples also showed a significant correlation between benign and later invasive ductal or lobular carcinoma in the same patient (cc = 0.607, p = 0.001). This data demonstrates that high risk HPV sequences of the same type are present in benign and subsequent non-invasive and invasive breast cancers in the same Australian patients, and these high risk HPVs in breast cancer are biologically active as shown by E7 immunohistochemistry. These findings suggest that high risk HPVs probably have oncogenic influences in a subset of breast cancers. Also, there is a correlation between the detection of HPV by both methods and this suggests that IHC may prove to be a reliable diagnostic tool for HPV.