To evaluate the effect of medical home implementation on primary care delivery in the Veterans Health Administration (VHA). We link interview-based qualitative data on medical home implementation to quantitative outcomes from VHA clinical encounter data. We use a longitudinal analysis with provider fixed effects (taking advantage of variation in timing of implementation and allowing each provider to serve as a control for him or herself) to test whether patient-aligned care team (PACT) implementation was associated with changes in organizational processes and patient outcomes. Among 683 PCPs, caring for 321,295 patients, the uptake of eight of nine PACT structural changes significantly increased from July 2010 to June 2012 as did the percentage of primary care appointments occurring by telephone and hospital discharges contacted within 2 days of discharge. We found that PACT implementation was associated with significant improvements in 2-day post-hospital discharge contact, but not primary care visits occurring by telephone or within 3days of the requested date. We found no association between medical home implementation and rates of emergency department use by patients. Medical home implementation at the VHA resulted in large changes in the structure of care but few changes in patient-level outcomes. These results highlight both the complexity of studying the effect of the medical home as well as implementing this model to change primary care delivery.