In the past two decades, relationships among health plans, medical groups, and providers have grown more complex and the number of clinical management strategies has increased. In this context, determining the independent effect of a particular organizational strategy on quality of care has become more difficult. The authors review some of the issues a researcher must address when studying the relationship between organizational characteristics and quality of care. They offer criteria for selecting a research question, list organizational characteristics that may influence quality, and suggest sampling and study design techniques to reduce confounding. Since this type of research often requires a health care organization as collaborator, the authors discuss strategies for developing research partnerships and collecting data from the partner organization. Finally, they offer suggestions for translating research into policy.