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Background The number of anal cancer diagnoses has been rising steadily, so that the incidence has doubled in the past 20 years. Almost all anal cancers are induced by persistent infection with human papillomaviruses. Hitherto the care of patients with anal cancer has been heterogeneous and little experience exists with the primary management of anal cancer. Methods The guideline was developed in accordance with the requirements of the German Guideline Program in Oncology. In line with the GRADE approach, the certainty of the evidence was assessed on the outcome level following a systematic literature search. Interdisciplinary working groups were set up to compile suggestions for recommendations, which were discussed and agreed upon in a formal consensus conference. Results Ninety-three recommendations and statements were developed. No high-quality evidence was available to support recommendations for or against the treatment of stage I anal cancer with local excision alone as an alternative to chemoradiotherapy. Chemoradiotherapy is the gold standard in the treatment of stages II–III. Among other aspects regarding the timing and extent of response evaluation after chemoradiotherapy, the guideline panel recommended against obtaining a biopsy in the event of complete clinical response. Owing to lack of confidence in the available evidence, only open recommendations were given for treatment of stage IV. Conclusion This evidence-based clinical practice guideline provides a sound basis for optimizing the interdisciplinary, cross-sector care of anal cancer patients. Among other areas, gaps in research were identified with respect to the care of patients with early-stage or metastatic anal cancer. Approaches such as chemoradiotherapy combined with regional deep hyperthermia require further investigation. The role for immunotherapy in the management of metastasized anal cancer has also been insufficiently explored to date.