The influence of potential prognostic factors (occupant- and crash-related factors, initial neck pain intensity and headache, whiplash injury severity, helplessness, locus of control, socioeconomic status) on neck pain intensity (VAS), disability (DRI), anxiety and depression (HADS) was estimated in a cohort of 3704 subjects with whiplash injury following a motor vehicle crash. Questionnaires were administered (baseline, 1-, 6-, 12-, 24-month follow-ups). VAS was trichotomized; "low" (0-30), "moderate" (31-54), "severe" (55-100). A cumulative logit model with a proportional odds assumption was applied. Results regarding depression differed somewhat from the other outcomes. Overall, initial neck pain intensity was an important prognostic factor, but acted also as an evident effect modifier. Females had slightly increased odds for all outcomes but depression, for which no gender differences were shown. Injury severity was associated with all outcomes, but was most pronounced regarding disability among those who perceived numbness/pain in arms/hands and also had severe initial neck pain (proportional odds ratio [OR] 6.5; 95% confidence interval [CI] 2.5-17.0). Initial headache influenced all outcomes. Income was not related to any of the outcomes, whereas a lower level of education was associated with all outcomes but depression. Locus of control was not a factor of importance. In contrast, helplessness was related to all outcomes, but was most pronounced regarding neck pain intensity and depression for subjects with severe initial neck pain (OR 4.8; 95% CI 2.9-7.8; OR 6.6; 95% CI 2.6-17.0). Associations seem to be established early, and then to be relatively constant over time.