Integrating immunotherapy, proton therapy and biological dose escalation into the definitive chemoradiation of oropharyngeal cancer poses several challenges. Reliable and reproducible data must be obtained in a timely fashion. However, despite recent international radiotherapy contouring guidelines, controversy persists as to the applicability of such guidelines to all cases. Similarly, a lack of consensus exists concerning both the definition of the organ at risk for oral mucositis and the most appropriate endpoint to measure for this critical toxicity. Finally, the correlation between early markers of efficacy such as complete response on PET CT following treatment and subsequent survival needs elucidation for biological subsets of oropharyngeal cancer.