The role of human papillomavirus in breast cancer pathogenesis is an area of considerable debate following differing results from all over the world. This study analyzed paraffin embedded tissue from 19 patients with benign or malignant breast disease. Standard PCR with GP5+/6+ and FAP primers, proved negative in all cases. However, qRT-PCR using the SF10 primer set detected HPV DNA in 2 out of these samples. Whilst our data does not support a major role for HPV in the pathogenesis of breast disease in Malta, it definitely does not exclude it totally. This study also clearly shows that the method of analysis is one of the variables resulting in the range of differing results witnessed worldwide in this area of study