Whiplash-associated disorders are common and incur considerable expense in social and economic terms. There are no known effective treatments for those people whose pain and disability persist beyond 3 months. We conducted a randomized, assessor-blinded, controlled trial at two centres in Australia. All participants received 3 advice sessions. In addition the experimental group participated in 12 exercise sessions over 6 weeks. Primary outcomes were pain intensity, pain bothersomeness and function measured at 6 weeks and 12 months. Exercise and advice was more effective than advice alone at 6 weeks for all primary outcomes but not at 12 months. The effect of exercise on the 0-10 pain intensity scale was -1.1 (95%CI -1.8 to -0.3, p=0.005) at 6 weeks and -0.2 (0.6 to -1.0, p=0.59) at 12 months; on the bothersomeness scale the effect was -1.0 (-1.9 to -0.2, p=0.003) at 6 weeks and 0.3 (-0.6 to 1.3, p=0.48) at 12 months. The effect on function was 0.9 (0.3 to 1.6, p=0.006) at 6 weeks and 0.6 (-0.1 to 1.4, p=0.10) at 12 months. High levels of baseline pain intensity were associated with greater treatment effects at 6 weeks and high levels of baseline disability were associated with greater treatment effects at 12 months. In the short-term exercise and advice is slightly more effective than advice alone for people with persisting pain and disability following whiplash. Exercise is more effective for subjects with higher baseline pain and disability.