A prospective study was used to: (1) quantify potential risk factors for whiplash associated disorder following a rear-end motor vehicle collision; and (2) develop a simple clinical decision rule for the early identification of patients at risk for long-term whiplash associated disorder. Between 1 October 1995 and 31 March 1998, 446 adults involved in rear-end collisions presented to the only two emergency departments serving Kingston, Ontario. Eligible and consenting subjects (n = 353) were contacted by telephone soon after the collisions then at multiple occasions up to 2 years post-collision. Bivariate and multiple logistic regression analyses were used to identify potential risk factors for persistent symptoms. A software package that uses Chi-squared automatic interaction detection and classification and regression trees was used to develop a simple clinical decision rule for the identification of patients at high and low risk for persistent whiplash associated disorder. Risk factors identified by regression analyses included: increased age, number of initial physical symptoms, and early development of the following symptoms: upper back pain, upper extremity numbness or weakness, or disturbances in vision. A simple clinical decision rule that requires asking up to three basic questions of each patient was derived and would have identified the 118 cases of persistent whiplash associated disorder with a sensitivity of 91.5% (95% confidence interval: 86.5, 96.6) and a specificity of 51.4% (44.7, 58.1). This study confirmed the importance of several risk factors for whiplash associated disorder following rear-end motor vehicle collisions.