Hand movement recovery and cortical reorganization were studied in 10 subjects with chronic stroke using functional MRI (fMRI) before and after training with an intensive finger movement tracking programme. Subjects were assigned randomly to a treatment or control group. The treatment group received 18-20 sessions of finger tracking training using target waveforms under variable conditions. The control group crossed over to receive the same treatment after the control period. For comparison with a healthy population, nine well elderly females were also studied; however, the well elderly controls did not cross over after the control period. The dependent variables consisted of a Box and Block score to measure prehensile ability (subjects with stroke only), a tracking accuracy score and quantification of active cortical areas using fMRI. For the tracking tests, the subjects tracked a sine wave target on a computer screen with extension and flexion movements of the paretic index finger. Functional brain images were collected from the frontal and parietal lobes of the subject with a 4 tesla magnet. Areas of interest included the sensorimotor cortex (SMC), primary motor area (M1), primary sensory area (S1), premotor cortex (PMC) and supplementary motor area (SMA). Comparison between all subjects with stroke and all well elderly subjects at pre-test was analysed with two-sample t-tests. Change from pre-test to post-test within subjects was analysed with paired t-tests. Statistical significance was set at P < 0.05. Stroke treatment subjects demonstrated significant improvement in tracking accuracy, whereas stroke control subjects did not until after crossover treatment. At pre-test, the cortical activation in the subjects with stroke was predominantly ipsilateral to the performing hand, whereas in the well elderly subjects it was contralateral. Activation for the stroke treatment group following training switched to contralateral in SMC, M1, S1 and PMC. The stroke control group's activation remained ipsilateral after the control period, but switched to contralateral after crossover to receive treatment. All well elderly subjects maintained predominantly contralateral activation throughout. Transfer of skill to functional activity was shown in significantly improved Box and Block scores for the stroke treatment group, with no such improvement in the stroke control group until after crossover. We concluded that individuals with chronic stroke receiving intensive tracking training showed improved tracking accuracy and grasp and release function, and that these improvements were accompanied by brain reorganization.