Cross-sectional investigation of muscle changes in patients suffering from persistent whiplash-associated disorders (WAD). To quantitatively compare the presence of fatty infiltrate in the cervical extensor musculature in a cohort of chronic whiplash patients (WAD II) and healthy control subjects across muscle and cervical segmental level. Magnetic resonance imaging (MRI) can be regarded as the gold standard for muscle imaging; however, there is little knowledge about in vivo features of neck extensor muscles in patients suffering from persistent WAD and how fat content alters across the factors of muscle, vertebral segments, age, self-reported pain and disability, compensation status, body mass index, and duration of symptoms. A reliable MRI measure for fatty infiltrate was performed of the cervical extensor muscles bilaterally in 113 female subjects (79 WAD, 34 healthy control; 18-45 years, 3 months to 3 years post injury). The measure was performed on all subjects for the rectus capitis posterior minor and major, multifidus, semispinalis cervicis and capitis, splenius capitis, and upper trapezius. The WAD subjects had significantly larger amounts of fatty infiltrate for all of the cervical extensor muscles compared with healthy control subjects (all P < 0.0001). In addition, the amount of fatty infiltrate varied by both cervical level and muscle, with the rectus capitis minor/major and multifidi at C3 having the largest amount of fatty infiltrate (P < 0.0001). Intramuscular fat was independent of age, self-reported pain/disability, compensation status, body mass index, and duration of symptoms. There is significantly greater fatty infiltration in the neck extensor muscles, especially in the deeper muscles in the upper cervical spine, in subjects with persistent WAD when compared with healthy controls. Future studies are required to investigate the relationships between muscular alterations and symptoms in patients suffering from persistent WAD.