The current guidelines of evidence-based medicine (EBM) presuppose that clinical research and clinical practice should advance from rigorous scientific tests as they generate reliable, value-free knowledge. Under this presupposition, hypotheses postulated by doctors and patients in the process of their decision making are preferably tested in randomized clinical trials (RCTs), and in systematic reviews and meta-analyses summarizing outcomes from multiple RCTs. Since testing under this scheme is predominantly focused on the criteria of generality and precision achieved through methodological rigor, at the cost of the criterion of realism, translating test results to clinical practice is often problematic. Choices concerning which methodological criteria should have priority are inevitable, however, as clinical trials, and scientific research in general, cannot meet all relevant criteria at the same time. Since these choices may be informed by considerations external to science, we must acknowledge that science cannot be value-free in a strict sense, and this invites a more prominent role for value-laden considerations in evaluating clinical research. The urgency for this becomes even more apparent when we consider the important yet implicit role of scientific theories in EBM, which may also be subjected to methodological evaluation and for which selectiveness in methodological focus is likewise inevitable.