Cervical muscle function is disturbed in patients with persistent pain related to a whiplash associated disorder (WAD) but little is known about neck extensor muscle morphometry in this group. This study used magnetic resonance imaging to measure relative cross-sectional area (rCSA) of the rectus capitis posterior minor and major, multifidus, semispinalis cervicis and capitis, splenius capitis and upper trapezius muscles bilaterally at each cervical segment. In total, 113 female subjects (79 WAD, 34 healthy control; 18-45 years, 3 months-3 years post-injury) were recruited for the study. Significant main effects for differences in muscle and segmental level were found between the two groups (P < 0.0001) as well as a significant group * muscle * level interaction (P < 0.0001). The cervical multifidus muscle in the WAD group had significantly larger rCSA at all spinal levels and in contrast, there were variable differences in rCSA measures across levels in the intermediate and superficial extensor muscles when compared to the healthy controls (P < 0.0001). There were occasional weak, although statistically significant relationships between age, body mass index (BMI), duration of symptoms and the size of some muscles in both healthy control and WAD subjects (P < 0.01). It is possible that the consistent pattern of larger rCSA in multifidus at all levels and the variable pattern of rCSA values in the intermediate and superficial muscles in patients with WAD may reflect morphometric change due to fatty infiltrate in the WAD muscles. Future clinical studies are required to investigate the relationships between muscular morphometry, symptoms and function in patients with persistent WAD.