Background. Understanding mechanisms of recovery may result in new treatment strategies to improve motor outcome after stroke. Imaging techniques such as functional magnetic resonance imaging (fMRI) and positron emission tomography (PET) allow changes in brain activity after stroke recovery to be identified. Objective. To systematically review serial imaging studies on recovery within 6 months poststroke, assess their methodological quality, and identify trends in the association between task-related brain activation patterns and functional upper limb recovery. Methods. A literature search was performed using Medline, PICARTA, and EMBASE databases. Studies were appraised using binary weighted methodological criteria for internal, statistical, and external validity. Results. Twenty-two of the 869 identified studies met the inclusion criteria. Studies showed methodological weaknesses with respect to controlling for task performance, selecting appropriate outcome measures, and adequate presentation and execution of statistical analysis. After stroke, motor task performance shows unilateral overactivation of motor and nonmotor areas, a posterior shift in activity in the primary motor cortex, and bilateral recruitment of associated motor and nonmotor areas. Concomitant with neurological recovery, overactivation appears to diminish longitudinally, but not in all patients. Conclusion. Despite methodological shortcomings and heterogeneity, trends can be discerned. However, statistically sound associations with recovery are not consistent. The challenges in future research will be, controlling for confounding factors, finding outcomes that specifically measure dexterity of the paretic limb, to control for the extent of white matter damage and changes in perfusion in order to establish the longitudinal construct validity of fMRI and PET with regard to upper limb recovery after stroke. © The Author(s) 2010.