BACKGROUND: A usual question from pediatrics emergence in public hospitals leads to evidence-based medicine (EBM), a new paradigm for medical education and practice. However, although canonical texts have presented EBM apologetically, a lot of criticism has resulted in controversy involving its supporters and opponents. OBJECTIVES: To provide a better understanding of EBM based on historical analyses of its controversies. METHODS: Historical analysis of controversies about EBM. MATERIALS: Primary and secondary sources on EBM from international medical journals. Results: The hierarchy of evidence that forms the epistemic basis of EBM has been strongly contested by its opponents; the interest and involvement of biomedical and pharmaceutical corporations on the trials has been denounced; as well as the prevalence of algorithmic approaches instead of comprehensive and humanized forms of care, with the consequent loss of the physician's professional autonomy and their submission to protocols. CONCLUSIONS: EBM is much more than rational and objective search, evaluation and clinical application of the "best" scientific evidence published in medical journals. A better understanding of its historical, epistemic, ethical, political and social aspects and dimensions allow us to balance the impact of prevailing technoscientific influences on medical education and clinical practice.