INTRODUCTION Personal and professional values of health-care practitioners influence their clinical decisions. AIM To investigate how medical students' values influence their clinical decisions. METHODS Values of 117 medical students were measured using an instrument we developed, the Healthcare Practitioner Values Scale. Factors that students consider in clinical decision-making were identified in four clinical scenarios using qualitative coding. Differences in values between students who considered given factors in decision-making and students who did not consider the same factors were analysed. Random effects models were used to investigate which differences were explained by variation in the clinical scenarios and factors considered in decision-making. RESULTS Six factors that students consider in clinical decision-making were identified and grouped into three categories: patient-centred (patient perspective, family and social circumstances); clinical (patient safety, symptoms and treatment efficacy); and situational factors (health-care practitioner self-awareness and service cost). Students who prioritised spirituality placed more emphasis on patient-centred factors, and less emphasis on clinical factors in different scenarios; students who prioritised critical thinking placed less emphasis on patient-centred factors; and students who prioritised capability, professionalism and safety values placed more emphasis on situational factors. Total proportion of variance in value differences explained by factors and clinical scenarios was 25.2% for spirituality and 56.2% for critical thinking. DISCUSSION Students who prioritise different values consider different factors in their clinical decisions. Spirituality and critical thinking values are more likely to influence students' decision-making approaches than other values. Improving students' awareness of how their own values influence their decisions can help them improve their clinical decision-making.