Evidence-based medicine (EBM) is beset with numerous problems. In addition to the fact that varied audiences have each customarily sought differing types of evidence, EBM traditionally incorporated a hierarchy of clinical research designs, placing systematic reviews and meta-analyses at the pinnacle. Yet the canonical pyramid of EBM excludes numerous sources of research information, such as basic research, epidemiology, and health services research. Models of EBM commonly used by third party payers have ignored clinical judgment and patient values and expectations, which together form a tripartite and more realistic guideline to effective clinical care. Added to this is the problem in which enhanced placebo treatments in experimentation may obscure verum effects seen commonly in practice. Compounding the issue is that poor systematic reviews which comprise a significant portion of EBM are prone to subjective bias in their inclusion criteria and methodological scoring, shown to skew outcomes. Finally, the blinding concept of randomized controlled trials is particularly problematic in applications of physical medicine. Examples from the research literature in physical medicine highlight conclusions which are open to debate. More progressive components of EBM are recommended, together with greater recognition of the varying audiences employing EBM.