BACKGROUND: Little is known about the most important organizational factors and strategies for transforming primary care clinics into patient-centered medical homes (PCMHs), so we studied this in newly certified medical homes in Minnesota. METHODS: We collected the following information from the first 120 clinics serving adults to be certified: (1) a 105-item survey about the presence and function of practice systems now and 3 years ago; (2) standardized composite clinic performance measures for diabetes and cardiovascular disease; and (3) a 44-item survey about PCMH transformation derived from 31 qualitative interviews about barriers, facilitators, and change strategies with participants from 9 diverse clinics. RESULTS: The response rates for the systems survey was 92.5% and was 98.3% for the survey about transformation. Nearly all the items from the qualitative interviews identified as potentially important for transformation were strongly endorsed. Eighteen items in this survey also correlated significantly (P = <.01) with change in practice systems at the level of r >/= 0.20. However, there was little relationship between these items and either absolute levels of systems or performance on composite measures of diabetes or vascular disease quality outcomes. CONCLUSIONS: Many items in the survey about transformation seem to have face validity for leaders of certified PCMHs and to be associated with the extent to which their clinics have made systems changes. While clinics may need to find their own unique path to transformation, the items identified here should be considered in those decisions.