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Background Understanding uncertainty in participatory decision-making requires scientific attention to interaction between what actually happens when patients, families and clinicians engage one another in conversation and the multi-level contexts in which these occur. Achieving this understanding will require conceptually grounded and scalable methods for use in large samples of people representing diversity in cultures, speaking and decision-making norms, and clinical situations. Discussion Here, we focus on serious illness and describe Conversational Stories as a scalable and conceptually grounded framework for characterizing uncertainty expression in these clinical contexts. Using actual conversations from a large direct-observation cohort study, we demonstrate how natural language processing and unsupervised machine learning methods can reveal underlying types of uncertainty stories in serious illness conversations. Conclusions Conversational Storytelling offers a meaningful analytic framework for scalable computational methods to study uncertainty in healthcare conversations.