Background: Whiplash-associated disorders (WAD) are common after motor vehicle collisions and can result in persistent pain and disability. Most affected individuals are classified as WAD grade II (WADII) and frequently exhibit sensory disturbances suggestive of peripheral nerve involvement. Although peripheral neuroinflammation has been implicated, related microstructural changes remain unknown.Methods: Diffusion tensor imaging (DTI) was used to assess the brachial plexus roots, C5–C8 spinal nerve roots, and median nerve in 102 participants with WADII within 4 weeks of injury and 37 healthy controls. Fifty-one participants returned for follow-up at 6 months. Associations between DTI metrics, clinical measures, and recovery were examined.Findings: Acute WADII participants showed increased axial diffusivity (AD) in the bilateral C6–C7 brachial plexus roots, persisting at 6 months. In the median nerve, mean diffusivity (MD), AD, and radial diffusivity (RD) were elevated at both time points. Conversely, bilateral C6–C8 spinal nerve roots showed increased fractional anisotropy and reduced MD and RD acutely and at follow-up, with AD decreasing at 6 months. Acute DTI metrics did not predict recovery; however, higher median nerve AD and MD were associated with greater neuropathic pain severity at follow-up.Interpretation: WADII is associated with widespread, persistent alterations in peripheral nerve microstructure, consistent with altered axonal physiology and low-grade neuroinflammation rather than overt structural nerve injury. These findings support peripheral nervous system involvement in WADII and highlight the importance of evaluating neural contributions to persistent pain.