The purpose of this study was to investigate the human papillomavirus (HPV) infection rate in malignant and benign breast tumours in north-west Chinese patients. Unselected fresh tissue samples were extracted from 48 invasive breast carcinoma and 30 benign breast tumours between August 2009 and August 2010. We used real-time fluorescence quantitative PCR (FQ-PCR) and in situ hybridization to detect HPV 6, 11 and 16, 18 sequences targeting the E6, E7 open-reading frame. The presence of HPV 6, 11 was only demonstrated in the 3 (10%) benign phyllodes tumour specimens. No HPV infection was detected in all the 48 invasive breast carcinoma. Specifically, all the positive specimens were detected by in situ hybridization but not in FQ-PCR. In addition, we found that the positive specimens became negative after 3 months frozen at -70°C. HPV was absent in patients with breast tumours in north-west China.