OBJECTIVES: Data on economic burden of head & neck (H&N) and anal cancers in Germany is scarce. Human papillomavirus (HPV) infection is likely to be responsible for 16% to 72% of H&N cancer, and 84% of anal cancer. This study aimed to assess the annual management costs (hospitalisations, inpatient rehabilitations, sick leaves) associated with these HPV-related cancers from the German Statutory Health Insurance (SHI) perspective. METHODS: This study was based on the retrospective analysis of five German databases, which cover hospitalisations (German Federal Statistical Office-Destatis), major categories of treatment such as surgery, radiotherapy and medical (Institute for the Hospital Remuneration System-InEK), inpatient rehabilitations (German Public Pension Insurance-DRV) and sick leaves (Local-SHI-funds, Federal Ministry of Health). Associated number of cancers, health care resource use, and costs were identified and extracted using ICD-10 codes (H&N cancer: C01-C06, C09-C14, C32; anal cancer: C21). The HPV-related cancers total cost was estimated based on the percentage of each cancer and anatomical site likely to be attributable to HPV. RESULTS: In 2008, 69,631 hospitalisations for H&N and anal cancers were reported (92% due to H&N cancer), whereas the number of inpatient rehabilitations and sick leaves were 5,415 and 18,391, respectively. The estimated total cost associated with HPV-related H&N and anal cancers was €111 million, mainly represented by H&N cancer (74%). Hospitalisations, inpatient rehabilitations, and sick leaves, accounted for 82%, 4%, and 15% of total HPV-related cost, respectively. CONCLUSIONS: The estimated annual cost of HPV-related H&N and anal cancers contribute to a significant economic burden in Germany, appearing to be as important as cost of HPV-related cervical cancer, and should be considered when assessing health and economic benefits of HPV vaccination in both genders. Furthermore, this cost is likely to be underestimated since outpatient management cost is not included, and may be significant for these cancers.