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.