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To investigate the cerebral mechanisms underlying learning of motor skills, we assessed serial changes of brain activation patterns during a pursuit rotor (PR) task in 12 right-handed healthy subjects using functional near-infrared spectroscopy (fNIRS). The subjects performed the task with their right hand for 15-s, alternated with a 30-s rest period, for 18 repetitions (cycles 1 to 18). Gains in motor skill were evaluated by recording the time for which the stylus remained on the target. Performance improved with repetition of the task. Task-related increases of oxygenated hemoglobin (oxy-Hb) were observed around the predicted location of the sensorimotor cortices on both hemispheres. The increased oxy-Hb levels appeared to reduce with repetition of the task in the channels covering the left sensorimotor area. Furthermore, there was a significant correlation between PR task performance gain and the oxy-Hb signal in the left and right sensorimotor areas. Our results suggest that cortical activation in the sensorimotor cortex reflects changes in a number of factors including sensory feedback processing, correct motor commands, and perceptual or cognitive function during learning of a PR task. Therefore, changes in contralateral sensorimotor cortical activation may serve as a motor sequence learning biomarker for rehabilitation purposes or the prediction of recovery.