Unlike medications, the dissemination of surgical procedures into practice is not regulated. Before marketing, pharmaceutical products are required to be shown safe and efficacious in comparative clinical trials that use bias-reducing strategies designed to reduce the distortion of estimates of treatment effect by predispositions toward the investigational intervention or control. Unless an investigational device is involved, the corresponding process for surgical innovations is usually unregulated and therefore may not be based on adequate evidence. Given these differences, we sought to evaluate the state of clinical research on invasive procedures. We conducted a systematic review of publications from 1999 through 2008, which reported the results of studies evaluating the effects of invasive therapeutic procedures, focusing on trials that appeared to influence practice. Our objective was to determine what proportion of studies evaluating surgical procedures use a comparative clinical trial design and methods to control bias. This article reports our results and raises concerns about the methodologic, and therefore the ethical, quality of clinical research used to justify the implementation of surgical procedures into practice.