A new cluster arousal analysis system was developed to quantify microdisturbances in the sleep architecture. The system was evaluated in 10 healthy volunteers and the sleep of 23 outpatients with chronic low back pain was investigated before and after a special rehabilitative training. The comparison of sleep parameters before and after the treatment showed a significant reduction of the cluster disturbed sleep (CDS), whereas sleep efficiency and the number of stage shifts remained unchanged. The reduction of the CDS correlated with a reduction of depression scale. This cluster arousal analysis appears to be a sensitive tool for evaluating alterations in the sleep microstructure.