The aim of this study was to explore whether reported pain and functional disability in whiplash-associated disorders (WAD) patients is associated with lesions to specific soft tissue structures in the upper cervical spine, as assessed by MRI. Pre-selected structures for MRI assessment included the alar ligaments, the transverse ligament, the tectorial and the posterior atlanto-occipital membranes. The questionnaire employed was a modification of the Oswestry Low Back Pain Index. It was comprised of ten single items related to pain and activity of daily living. Ninety-two whiplash patients and 30 control persons, randomly drawn, were included. WAD patients reported significantly more pain and functional disability than the controls, both for total score and each of the ten single items. In the WAD patients, MRI lesions to the alar ligaments showed the most consistent association to the reported pain and disability. Lesions to other structures often occurred in combination with lesions to the alar ligaments. Lesions to the transverse ligament and to the posterior atlanto-occipital membrane also appeared to be related to the NDI score, although the association was weaker than for the alar ligament. The disability score increased with increasing number of abnormal (grade 2-3) structures. These results indicate that symptoms and complaints among WAD patients can be linked with structural abnormalities in ligaments and membranes in the upper cervical spine, in particular the alar ligaments.