With so much emphasis from government and private insurers on the need to lower the cost of medical care, comparative effectiveness research (CER) has come into its own. CER aims to compare two or more existing treatment regimens to determine which are most cost-effective. Since so many sophisticated software tools are now available to help facilitate such research, healthcare IT executives need to stay well-informed about the strengths and limitations of CER. In the past, I've written about Clinical Query, a searchable patient data repository being used by Boston's Beth Israel Deaconess Medical Center to facilitate CER.