Background: Biomechanical measures quantify motor control and functional deficits in Whiplash Associated Disorders (WAD), but few studies relate those measures to the clinical scales that are routinely used to assess patients. Most studies are limited to chronic neck pain, and report poor to moderate correlations. Objective: To define a statistical model that relates measures of neck kinematics with clinical scales of neck pain, in WAD patients during the rehabilitation process in the acute phase (less than 3 months since the accident). Methods: 96 WAD patients self-assessed their pain using VAS and NPQ, and passed neck motion tests as part of their rehabilitation program. Four regression models were fitted to analyze the effects of the measured kinematic parameters and subject-specific characteristics on VAS and NPQ. Model errors were compared to minimal clinically significant differences. Results: Multiple correlation coefficients of the models were between 0.74 and 0.90. More than 66% of that correlation was accounted for by subject-specific factors, and most of the other half by the measured kinematic parameters. Range of motion of flexion-extension and axial rotation, and harmonicity of flexion-extension, where the variables most consistently related to the decrease of pain. The error of the models was within the MCSD in more than 50% of the observations. Conclusions: Part of the individual progression of pain and pain-related disability in acute WAD patients, as rated by NPQ and VAS, can be mapped to objective kinematic parameters of neck mobility tests, like ranges of motion, velocities, repeatability and harmonicity of movements.