We used a perturb-and-measure approach, by combining transcranial magnetic stimulation (TMS) and positron emission tomography (PET), to examine changes in the primary motor area (M1) and its effective connectivity in stroke patients with chronic motor deficits (>1-year post-stroke) who underwent 3 weeks of constraint-induced movement therapy. During the 3-week period, 7 patients spent 4 h per day performing shaping exercises with the affected arm under our supervision for 14 days and wore a mitt on the unaffected arm at home in situations where safety was not compromised. Anatomical magnetic resonance imaging confirmed that all patients had lesions that encompassed the white matter; no patient had damage in the hand representation of M1. Improvements on various motor tests were observed immediately after therapy and 1 month afterwards. During the TMS/PET sessions, we applied trains of subthreshold 10-Hz repetitive TMS over the hand representation of the ipsilesional and contralesional M1s and varied the number of TMS trains delivered during each scan. The results demonstrate changes in the local response of TMS in the ipsilesional and contralesional M1, changes in the strength of interhemispheric connectivity between M1s, and changes in the effective connectivity of the ipsilesional and contralesional M1s with the non-primary motor areas, the basal ganglia, and the motor nuclei of the thalamus.