Although rheumatology has been on the cutting edge of health services research for decades, there are many unresolved issues for patients, clinicians, insurers, and policy makers. This article explore three areas in which methodologic controversies present tradeoffs to a health care system that is grappling with larger issues around cost and access to care. Specifically, we examine issues around the use of large databases, the appropriate instruments for measuring patient-centered outcomes, and the questions that are raised from cost effectiveness studies of new treatments for rheumatoid arthritis (RA). The issues are presented in the context of a need to provide better information to those who are providing care and those who are paying for it.