The researchers' assumptions invariably influence research outcomes. This is true for both qualitative and quantitative studies. Assumptions or choices regarding underlying theories, causal relations, study setting and population, sampling strategies, participant non-response, data collection, data analysis, and researchers' perceptions and interpretations of results are among factors that can induce uncertainty in research findings. Researchers tend to treat these factors as potential study limitations, but how they may impact research findings is rarely explicated and, therefore, mostly unknown. In this article, we approach uncertainty as unavoidable in research and argue that communicating about uncertainty can inform researchers, policy makers and practitioners about the validity and applicability of the study findings for their interests and contexts. We illustrate approaches to address, interpret, and explicate uncertainty in medical education research in both qualitative and quantitative paradigms. Across research paradigms, we call on researchers to consider the uncertainty in their research findings, employ appropriate methods to explore its extent and effects in their work, and communicate it explicitly in their research papers. This will help to advance our understanding of the nature and implications of the emerging knowledge in our field.