BACKGROUND: Research connecting patient-centered medical homes (PCMHs) with improved quality and reduced utilization is inconsistent, possibly because individual domains of change, and the stage of change, are not incorporated in the research design. The objective of this study was to examine the association between stage and domain of change and patterns of health care utilization. METHODS: This was a cross-sectional observational study that including 87 Minnesota clinics certified as medical homes. Patients included those receiving management for diabetes or cardiovascular disease with insurance coverage by payers participating in the study. PCMH transformation stage was defined by practice systems in place, with measurements summarized in 5 domains. Health care utilization was measured by total utilization, frequency of outpatient visits and prescriptions, and occurrence of inpatient and emergency department visits. RESULTS: PCMH transformation was associated with few changes in utilization, but there were important differences by the underlying domains of change. We demonstrate meaningful differences in the impact of PCMH transformation by diagnosis cohort and comorbidity status of the patient. CONCLUSIONS: Because the association of health care utilization with PCMH transformation varied by transformation domain and patient diagnosis, practice leaders need to be supported by research incorporating detailed measures of PCMH transformation.