The evidence-based practice and evidence-based medicine movements have promoted standardization through guideline development methodologies based on systematic reviews and meta-analyses of best available research. EBM has challenged clinicians to question their reliance on practical reasoning and clinical judgement. In this paper, we argue that the protagonists of EBM position their mission as reducing uncertainty through the use of standardized methods for knowledge evaluation and use. With this drive towards uniformity, standardization and control comes a suspicion towards intuition, creativity and uncertainty as integral parts of medical practice. We question the appropriateness of attempts to standardize professional practice through a discussion of the importance of uncertainty. Greenhalgh’s taxonomy of uncertainty is used to inform an analysis of the clinical reasoning occurring in a potentially life threatening emergency situation with a young patient. The case analysis is further developed by the use of the Canadian philosopher Bernard Lonergan’s theory about understanding and objective knowing. According to Lonergan it is not by getting rid of or even by reducing uncertainty, but by attending systematically to it and by relating to it in a self-conscious way, that objective knowledge can be obtained. The paper concludes that uncertainty is not a regrettable and unavoidable aspect of decision making but a productive component of clinical reasoning.