We describe the illness perceptions of patients with low back pain, how they change over 6 months, and their associations with clinical outcome. Consecutive patients consulting eight general practices were eligible to take part in a prospective cohort study, providing data within 3 weeks of consultation and 6 months later. Illness perceptions were measured using the Revised Illness Perception Questionnaire (IPQ-R). Clinical outcome was defined using the Roland and Morris Disability Questionnaire (RMDQ) and patients' global rating of change. Associations between patients, perceptions and poor outcome were analysed using unadjusted and adjusted risk ratios (RR) and 95% confidence intervals. 1591 completed questionnaires were received at baseline and 810 at 6 months. Patients had a mean age of 44 years and 59% were women. Mean (SD) RMDQ score at baseline was 8.6 (6.0) and 6.2 (6.1) at 6 months. 52% and 41% of patients had a poor clinical outcome at 6 months using RMDQ and global rating scores, respectively. There were strong, statistically significant, associations (RRs of 1.4 and over) between IPQ-R baseline consequences, timeline acute/chronic, personal control and treatment control scores and poor outcome. Patients who expected their back problem to last a long time, who perceived serious consequences, and who held weak beliefs in the controllability of their back problem were more likely to have poor clinical outcomes 6 months after they consulted their doctor. These results have implications for the management of patients, and support the need to assess and address patients' cognitions about their back problems.