Head and neck cancers centered at the base of skull are better visualized on MRI than on CT. The purpose of this investigation was to investigate the accuracy of bulk density assignment in head and neck intensity‐modulated radiation therapy (IMRT) treatment plan optimization. Our study investigates dose calculation differences between density‐assigned MRI and CT, and identifies potential limitations related to dental implants and MRI geometrical distortion in the framework of MRI‐only‐based treatment planning. Bulk density assignment was performed and applied onto MRI to generate three MRI image sets with increasing levels of heterogeneity for seven patients: 1) MRInormalW: all water‐equivalent; 2) MRIW + B: included bone with density of 1.53 normalg/cm3; and 3) MRIW + B + A: included bone and air. Using identical planning and optimization parameters, MRI‐based IMRT plans were generated and compared to corresponding, forward‐calculated, CT‐based plans on the basis of target coverage, isodose distributions, and dose‐volume histograms (DVHs). Phantom studies were performed to assess the magnitude and spatial dependence of MRI geometrical distortion. MRInormalW‐based dose calculations overestimated target coverage by 16.1%. Segmentation of bone reduced differences to within 2% of the coverage area on the CT‐based plan. Further segmentation of air improved conformity near air–tissue interfaces. Dental artifacts caused substantial target coverage overestimation even on MRIW + B + A. Geometrical distortion was less than 1 mm in an imaging volume 20 × 20 × 20 cm3 around scanner isocenter, but up to 4 mm at 17 cm lateral to isocenter. Bulk density assignment in the framework of MRI‐only IMRT head and neck treatment planning is a feasible method with certain limitations. Bone and teeth account for the majority of density heterogeneity effects. While soft tissue is well visualized on MRI compared to CT, dental implants may not be visible on MRI and must be identified by other means and assigned appropriate density for accurate dose calculation. Far off‐center geometrical distortion of the body contour near the shoulder region is a potential source of dose calculation inaccuracy.PACS numbers: 87.61.‐c, 87.55.‐D