Human papillomavirus (HPV) is an important factor for the development of tonsillar squamous cell carcinoma (TSCC). In addition, patients with HPV‐positive TSCC have a better clinical outcome than patients with HPV‐negative TSCC. Although, HPV is an important prognostic marker, additional biomarkers are needed to better predict clinical outcome to individualize treatment. Hence, we examined if classical HLA HLA‐A,B,C and nonclassical HLA‐E,G could serve as such marker. Formalin‐fixed paraffin‐embedded TSCC from 150 patients diagnosed 2000–2006, earlier analyzed for HPV DNA and p16INK4a, and treated with intention to cure were evaluated for the expression of HLA‐A,B,C and HLA‐E,G by immunohistochemistry. For HPV‐positive TSCC a low expression of HLA‐A,B,C, whereas for HPV‐negative TSCC, a normal expression of HLA‐A,B,C was significantly correlated to a favorable clinical outcome. These correlations were more pronounced for membrane staining of HLA‐A,B,C when compared with cytoplasmatic staining. No significant correlation was found between HLA‐E,G and HPV status or clinical outcome. The unexpected contrasting correlation between HLA‐A,B,C expression, and clinical outcome depending on HPV, indicates essential differences between HPV‐positive and HPV‐negative TSCC. Furthermore, our data demonstrate that for both HPV‐positive and HPV‐negative TSCC, the expression of HLA‐A,B,C together with HPV may serve as a useful biomarker for predicting clinical outcome.