It is impossible to answer every potential clinical question through randomized controlled trials. Hence, assumptions, rational thinking, logic, and reasoning are used in making recommendations; however, these methods may interfere with the judicious application of evidence-based medicine and, as discussed in this article, may result in logical fallacies. We also explain how we may incorporate recommendations based on assumptions and rational thinking in patient care. Extrapolations of study content and confusing association with causation are common pitfalls in the application of the evidence-based medicine process. Personal bias can be another barrier in the adoption of evidence-based medicine. It can be difficult to modify personal bias despite the evidence; keeping up with the medical literature in a busy practice can be daunting.