Longitudinal imaging studies of primary progressive multiple sclerosis (PPMS) have shown significant changes in MR measures over 1 to 2 years. Correlation with clinical change over the same period has not been evident; we investigated the possibility that this is because the period of observation was insufficient for these associations to become apparent. Forty-one patients with PPMS were followed prospectively for 5 years. Patients had clinical [Expanded Disability Status Scale (EDSS) and Multiple Sclerosis Functional Composite Measure (MSFC)] and MRI assessment (brain and spinal cord) at baseline, 1, 2 and 5 years. At 5 years, significant deterioration was seen in all clinical and MRI measures (P<0.01, P<0.001 respectively). Associations were seen between increase in EDSS score and decrease in cord area (r=0.31, P<0.05) and between increase in MSFC and both rate of ventricular enlargement (r=0.31, P<0.05) and increase in T2 load (r=0.31, P<0.05). The rates of change of MR measures were not associated with age or disease duration and were more consistent within than between patients. Longer duration of follow-up demonstrates modest associations between change in clinical and MR measures and provides new insights into the pattern of change within and between individuals with PPMS.