Abstract Studies have shown that students may feel emotional discomfort when they are asked to identify ethical problems which they have encountered during their training. Teachers in medical ethics, however, more often focus on the cognitive and rational ethical aspects and not much on students’ emotions. The purpose of this qualitative study was to explore students’ feelings and emotions when dealing with ethical problems during their clinical training and explore differences between two countries: Indonesia and the Netherlands. We observed a total of eighteen ethics group discussions and interviewed fifteen medical students at two medical schools. Data were interpreted and analyzed using content analysis. We categorized students’ negative emotions based on their objects of reflection and came up with three categories: emotions concerning their own performance, emotions when witnessing unethical behaviors, and emotions related to barriers and limitations of their working environment. Our study suggests that addressing emotional responses in a culturally sensitive way is important to develop students’ self-awareness. Teachers should be able to guide students to reflect on and be critical of their own thoughts and emotions, to understand their own moral values, especially when confronted with other individuals.