Health reform legislation grants authority for patient-centered medical home pilot projects to test changes in the way primary care is provided. There is concern that using a measurement tool to qualify medical homes that is solely based on the presence or absence of "system elements" may miss the point conceptually and lead physicians astray in attempts to transform their entire practices. To find out whether and how practice characteristics explain health care quality, we examined risk-adjusted composite measures of quality for common chronic and acute care conditions and preventive care from 202 general internists working primarily in small primary care office settings. We found that current conceptions and measures of what constitutes "successful" practice systems and care are incomplete, and have limited associations with measures of health care quality. Future research should explore more fully the issues around physician competence, including competence in systems and quality improvement; the interactive nature of clinical practice; and other important system elements not captured by current tools.