Introduction: There is little empirical evidence on children's subjective experiences of discomfort during clinical research procedures. Therefore, Institutional Review Boards have limited empirical information to guide their decision-making on discomforts for children in clinical research. To get more insight into what children's discomforts are during clinical research procedures, we interviewed a group of children on this topic and also asked for suggestions to reduce possible discomforts. Materials and methods: Forty-six children (aged 6-18) participating in clinical research studies (including needle-related procedures, food provocation tests, MRI scans, pulmonary function tests, questionnaires) were interviewed about their experiences during the research procedures. Thematic analysis was used to analyze the interviews. Results: The discomforts of the interviewed children could be divided into two main groups: physical and mental discomforts. The majority experienced physical discomforts during the research procedures: pain, shortness of breath, nausea, itchiness, and feeling hungry, which were often caused by needle procedures, some pulmonary procedures, and food provocation tests. Mental discomforts included anxiousness because of anticipated pain and not knowing what to expect from a research procedure, boredom and tiredness during lengthy research procedures and waiting, and embarrassment during Tanner staging. Children's suggestions to reduce the discomforts of the research procedures were providing distraction (e.g. watching a movie or listening to music), providing age-appropriate information and shortening the duration of lengthy procedures. Discussion: Our study shows that children can experience various discomforts during research procedures, and it provides information about how these discomforts can be reduced according to them. Further research is needed with larger samples to study the number of children that experience these mentioned discomforts during research procedures in a quantitative way.