While studies have demonstrated the cervical facet capsule is at risk for tensile injury during whiplash, the relationship between joint loading, changes in the capsule’s structure, and pain is not yet fully characterized. Complementary approaches were employed to investigate the capsule’s structure-function relationship in the context of painful joint loading. Isolated C6/C7 facet joints (n=8) underwent tensile mechanical loading, and measures of structural modification were compared for two distraction magnitudes: 300 μm (PV) and 700 μm (SV). In a matched in vivo study, C6/C7 facet joints (n=4) were harvested after the same SV distraction and the tissue was sectioned to analyze collagen fiber organization using polarized light microscopy. Laxity following SV distraction (7.30±3.01%) was significantly greater (p<0.001) than that produced following PV distraction (0.99±0.44%). Also, SV distractions produced significantly higher maximum principal strain (p<0.001) in the capsule and resulted in significantly greater decreases in stiffness (p=0.002) when compared to PV distraction. After SV distraction in vivo, mean angular deviation of the fiber direction (16.8±2.6º) was significantly increased (p=0.004) relative to naive samples in the lateral region of the capsule, indicating collagen fiber disorganization. These findings demonstrate that certain subfailure loading conditions are associated with altered joint mechanics and collagen fiber disorganization and imply ligament damage. Substructural damage in the capsule has the potential to both directly modulate nerve fiber signaling and produce sustained physiologic modifications that may initiate persistent pain.