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Background and Purpose: Hypoxia Positron-Emission-Tomography (PET) as well as Computed Tomography (CT) radiomics have been shown to be prognostic for radiotherapy outcome. Here, we investigate the stratification potential of CT-radiomics in head and neck cancer (HNC) patients and test if CT-radiomics is a surrogate predictor for hypoxia as identified by PET., Materials and Methods: Two independent cohorts of HNC patients were used for model development and validation, HN1 (n = 149) and HN2 (n = 47). The training set HN1 consisted of native planning CT data whereas for the validation cohort HN2 also hypoxia PET/CT data was acquired using [ 18 F]-Fluoromisonidazole (FMISO). Machine learning algorithms including feature engineering and classifier selection were trained for two-year loco-regional control (LRC) to create optimal CT-radiomics signatures.Secondly, a pre-defined [ 18 F]FMISO-PET tumour-to-muscle-ratio (TMR peak  ≥ 1.6) was used for LRC prediction. Comparison between risk groups identified by CT-radiomics or [ 18 F]FMISO-PET was performed using area-under-the-curve (AUC) and Kaplan-Meier analysis including log-rank test., Results: The best performing CT-radiomics signature included two features with nearest-neighbour classification (AUC = 0.76 ± 0.09), whereas AUC was 0.59 for external validation. In contrast, [ 18 F]FMISO TMR peak reached an AUC of 0.66 in HN2. Kaplan-Meier analysis of the independent validation cohort HN2 did not confirm the prognostic value of CT-radiomics (p = 0.18), whereas for [ 18 F]FMISO-PET significant differences were observed (p = 0.02)., Conclusions: No direct correlation of patient stratification using [ 18 F]FMISO-PET or CT-radiomics was found in this study. Risk groups identified by CT-radiomics or hypoxia PET showed only poor overlap. Direct assessment of tumour hypoxia using PET seems to be more powerful to stratify HNC patients., Competing Interests: The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: DT and DZ declare institutional collaborations including financial support with the companies Siemens Healthineers (2014–2019), Elekta AB, Philips and PTW Freiburg without any direct relation to this study. In the past 5 years, MB attended an advisory board meeting of MERCK KGaA (Darmstadt), for which the University of Dresden received a travel grant. He further received funding for his research projects and for educational grants to the University of Dresden by Teutopharma GmbH (2011–2015), IBA (2016), Bayer AG (2016–2018), Merck KGaA (2014–2030), Medipan GmbH (2014–2018). For the German Cancer Research Center (DKFZ, Heidelberg) MB is on the supervisory boards of HI-STEM gGmbH (Heidelberg). MB, as former chair of OncoRay (Dresden) and present CEO and Scientific Chair of the German Cancer Research Center (DKFZ, Heidelberg), signed/signs contracts for his institute(s) and for the staff for research funding and/or collaborations with a multitude of companies worldwide. MB confirms that none of the above funding sources were involved in the design of this study, the preparation of this paper, the materials used, or the collection, analysis, and interpretation of data., (© 2020 The Author(s).)