Uncertainty is a common and increasingly acknowledged problem in clinical practice. Current single best answer (SBA) style assessments test areas where there is one correct answer, and as the approach to assessment impacts on the approach to learning, these exams may poorly prepare our future doctors to handle uncertainty. We therefore, need to modify our approach to assessment to emphasize reasoning and introduce the possibility of more than one 'correct' answer. We have developed clinical prioritization questions (CPQs), a novel formative assessment tool in which students prioritize possible responses in order of likelihood. This assessment format was piloted with a group of medical students and evaluated in comparison with the more traditional SBA question format in a team-based learning setting. Students reported that they felt ongoing use would help improve their tolerance of uncertainty (p < 0.01). Furthermore, over 80% of students felt that CPQs were more reflective of real-life clinical practice. Group based discussions were significantly longer when answering CPQs (p < 0.01), suggesting they may promote richer discourse. CPQs may have a role in formative assessment to help equip students with the skills to cope with ambiguity and strengthen clinical reasoning and decision-making. Institutions may find them more practical to implement compared with other clinical reasoning assessment tools.