The Affordable Care Act establishes a new public-private institute (PCORI) to coordinate research on the comparative effectiveness of medical interventions. To address fears that this initiative would lead to interference with the doctor-patient relationship, the ACA contains language limiting how research findings can be used.  The law gives PCORI no authority to mandate coverage or reimbursement decisions. Whether this initiative will ultimately affect clinical practice and help bend the health care cost curve (or even stick politically) remains an open question. Drawing on case studies, elite interviews, and public opinion surveys, this paper examines how partisan polarization, electoral competition and blame avoidance behavior has led to the politicization of evidence-based medicine. Until recently, evidence-based medicine was a technocratic, third-tier issue. Democratic and Republican health experts in agencies, think tanks and universities agreed that providers, payers, and patients need reliable information about what treatments work best for what patients, but the issue failed to capture the attention of the mass public. During the first Obama Administration, EBM got caught up in the wider political struggle over national health reform. Comparative effectiveness research morphed from being a low profile valence issue to a highly contested position issue as critics charged that the Obama Administration was promoting “rationing.” The CER story is a cautionary tale of how elite polarization can politicize and undermine research-based problem solving in contemporary American government.