Background: Autocontouring improves workflow in computed tomography (CT)-based dose planning, but could also potentially play a role for optimal use of daily cone beam CT (CBCT) in adaptive radiotherapy. This study aims to determine the accuracy of a deformable image registration (DIR) algorithm for organs at risk (OAR) in the neck region, when applied to CBCT. Material and methods: For 30 head and neck cancer (HNC) patients 14 OARs including parotid glands, swallowing structures and spinal cord were delineated. Contours were propagated by DIR from CT to the CBCTs of the first and last treatment fraction. An indirect approach, propagating contours to the first CBCT and from there to the last CBCT was also tested. Propagated contours were compared to manually corrected contours by Dice similarity coefficient (DSC) and Hausdorff distance (HD). Dose was recalculated on CBCTs and dosimetric consequences of uncertainties in DIR were reviewed. Results: Mean DSC values of ≥0.8 were considered adequate and were achieved in tongue base (0.91), esophagus (0.85), glottic (0.81) and supraglottic larynx (0.83), inferior pharyngeal constrictor muscle (0.84), spinal cord (0.89) and all salivary glands in the first CBCT. For the last CBCT by direct propagation, adequate DSC values were achieved for tongue base (0.85), esophagus (0.84), spinal cord (0.87) and all salivary glands. Using indirect propagation only tongue base (0.80) and parotid glands (0.87) were ≥0.8. Mean relative dose difference between automated and corrected contours was within ±2.5% of planed dose except for esophagus inlet (-4.5%) and esophagus (5.0%) for the last CBCT using indirect propagation. Conclusion: Compared to manually corrected contours, the DIR algorithm was accurate for use in CBCT images of HNC patients and the minor inaccuracies had little consequence for mean dose in most clinically relevant OAR. The method can thus enable a more automated segmentation of CBCT for use in adaptive radiotherapy. Radiotherapy is the primary treatment for most patients with squamous cell carcinoma of the head and neck and about 80% of all patients receive radiotherapy either alone or in combination with surgery and chemotherapy. Relatively high loco-regional control rates are obtained, but at the expense of substantial side effects, of which xerostomia and swallowing dysfunction are the most prominent [1–4 Jensen K, Jensen AB, Grau C. A cross sectional quality of life study of 116 recurrence free head and neck cancer patients. The first use of EORTC H&N35 in Danish. Acta Oncol 2006;45:28–37. Jensen K, Lambertsen K, Grau C. Late swallowing dysfunction and dysphagia after radiotherapy for pharynx cancer: frequency, intensity and correlation with dose and volume parameters. Radiother Oncol 2007;85:74–82. Jensen K, Overgaard M, Grau C. Morbidity after ipsilateral radiotherapy for oropharyngeal cancer. Radiother Oncol 2007;85:90–7. Mortensen HR, Overgaard J, Specht L, et al. Prevalence and peak incidence of acute and late normal tissue morbidity in the DAHANCA 6&7 randomised trial with accelerated radiotherapy for head and neck cancer. Radiother Oncol 2012;103:69–75. ]. The observed morbidity is to a large extent due to inadvertent irradiation of normal tissues in the vicinity of the clinical target, including salivary glands and swallowing structures [5 Eisbruch A, Ten Haken RK, Kim HM, et al. Dose, volume, and function relationships in parotid salivary glands following conformal and intensity-modulated irradiation of head and neck cancer. Int J Radiat Oncol Biol Phys 1999;45:577–87. [CrossRef], [PubMed], [Web of Science ®] ,6 Langendijk JA, Doornaert P, Rietveld DH, et al. A predictive model for swallowing dysfunction after curative radiotherapy in head and neck cancer. Radiother Oncol 2009;90:189–95. [CrossRef], [PubMed], [Web of Science ®] ]. The irradiation of normal structures are in part a result of applied margins around the clinical target to counteract multiple uncertainties, including daily setup errors, target definition, and interfraction changes in the anatomy. Several studies indicate that the anatomical changes in these patients over the course of treatment can be substantial [7–9 Barker JL, Garden AS, Ang KK, et al. Quantification of volumetric and geometric changes occurring during fractionated radiotherapy for head-and-neck cancer using an integrated CT/linear accelerator system. Int J Radiat Oncol Biol Phys 2004;59:960–70. Castadot P, Lee JA, Geets X, et al. Adaptive radiotherapy of head and neck cancer. Semin Radiat Oncol 2010;20:84–93. Ricchetti F, Wu B, McNutt T, et al. Volumetric change of selected organs at risk during IMRT for oropharyngeal cancer. Int J Radiat Oncol Biol Phys 2011;80:161–8. ]. Repeated imaging and replanning, even with a single mid-treatment computed tomography (CT), can significantly improve tumor coverage and normal tissue sparing [10–12 Hansen EK, Bucci MK, Quivey JM, et al. Repeat CT imaging and replanning during the course of IMRT for head-and-neck cancer. Int J Radiat Oncol Biol Phys 2006;64:355–62. Schwartz DL, Garden AS, Thomas J, et al. Adaptive radiotherapy for head-and-neck cancer: initial clinical outcomes from a prospective trial. Int J Radiat Oncol Biol Phys 2012;83:986–93. Schwartz DL, Garden AS, Shah SJ, et al. Adaptive radiotherapy for head and neck cancer-dosimetric results from a prospective clinical trial. Radiother Oncol 2013;106:80–4. ]. Replanning requires repeated contouring of target volumes and normal tissues, which remains a time consuming task, even for experienced clinicians. There is a growing array of commercial software aimed at easing this burden by automatic contouring, utilizing novel deformable image registration (DIR) techniques to propagate one set of contours from an initial CT to fit the anatomy of a second CT [13 Elstrøm UV, Wysocka BA, Muren LP, et al. Daily kV cone-beam CT and deformable image registration as a method for studying dosimetric consequences of anatomic changes in adaptive IMRT of head and neck cancer. Acta Oncol 2010;49:1101–8. [Taylor & Francis Online], [Web of Science ®] ,14 Østergaard Noe K, De Senneville BD, Elstrøm UV, et al. Acceleration and validation of optical flow based deformable registration for image-guided radiotherapy. Acta Oncol 2008;47:1286–93. [Taylor & Francis Online], [Web of Science ®] ]. Such techniques have been found to reduce contouring time considerably [15 La Macchia M, Fellin F, Amichetti M, et al. Systematic evaluation of three different commercial software solutions for automatic segmentation for adaptive therapy in head-and-neck, prostate and pleural cancer. Radiat Oncol 2012;7:160. [CrossRef], [PubMed], [Web of Science ®] ,16 Teguh DN, Levendag PC, Voet PW, et al. Clinical validation of atlas-based auto-segmentation of multiple target volumes and normal tissue (swallowing/mastication) structures in the head and neck. Int J Radiat Oncol Biol Phys 2011;81:950–7. [CrossRef], [PubMed], [Web of Science ®] ]. Today, in-room daily imaging with cone beam CT (CBCT) allows more convenient soft tissue volumetric information to be potentially utilized in an adaptive approach. Previous studies have shown that if the image quality is sufficiently optimized, it is possible to contour soft tissue organs at risk (OAR), including spinal cord, salivary glands and swallowing structures [17 Elstrøm UV, Muren LP, Petersen JB, et al. Evaluation of image quality for different kV cone-beam CT acquisition and reconstruction methods in the head and neck region. Acta Oncol 2011;50:908–17. [Taylor & Francis Online], [Web of Science ®] ]. With Hounsfield unit calibration, the segmented CBCT can subsequently be used for dose calculation, with an overall precision of 2–3% for clinically relevant dose-volume parameters compared to standard CT-based dose planning [18 Elstrøm U, Olsen S, Wysocka B, et al. Cone-beam CT-based radiotherapy planning of head and neck cancer. Radiother Oncol 2012;103. [CrossRef] ]. Combining DIR techniques with the daily CBCT imaging could potentially enable prospective monitoring of volumetric and dosimetric changes over the course of treatment, improving the possibilities for plan adaptation. Few studies concerning this have been published to date [19 Hou J, Guerrero M, Chen W, et al. Deformable planning CT to cone-beam CT image registration in head-and-neck cancer. Med Phys Apr 2011;38:2088–94. [CrossRef], [PubMed], [Web of Science ®] ]. If feasible, this approach may also replace the mid-treatment CT as an added benefit. The purpose of this study was to determine the contouring accuracy of a software solution for unsupervised segmentation of OARs in daily CBCTs of head and neck cancer (HNC) patients.