Clinical management decisions for patients with cancer are increasingly being guided by prognostic and predictive markers. Use of these markers should be based on a sufficiently comprehensive body of unbiased evidence to establish that benefits to patients outweigh harms and to justify expenditure of health care dollars. Careful assessments of the clinical utility of markers by using comparative effectiveness research methods are urgently needed to more rigorously summarize and evaluate the evidence, but multiple factors have made such assessments difficult. The literature on tumor markers is plagued by nonpublication bias, selective reporting, and incomplete reporting. Several measures to address these problems are discussed, including development of a tumor marker study registry, greater attention to assay analytic performance and specimen quality, use of more rigorous study designs and analysis plans to establish clinical utility, and adherence to higher standards for reporting tumor marker studies. More complete and transparent reporting by adhering to criteria such as BRISQ [Biospecimen Reporting for Improved Study Quality] criteria for reporting details about specimens and REMARK [Reporting Recommendations for Tumor Marker Prognostic Studies] criteria for reporting a multitude of aspects relating to study design, analysis, and results, is essential for reliable assessment of study quality, detection of potential biases, and proper interpretation of study findings. Adopting these measures will improve the quality of the body of evidence available for comparative effectiveness research and enhance the ability to establish the clinical utility of prognostic and predictive tumor markers.