The participation of children in medical research raises many ethical issues, in particular regarding assent. However, little is known about children's own views on participation. This study presents results from interviews with children 10–12 years old with and without experience in a large-scale longitudinal screening study. We identified five themes: (1) knowledge about research, (2) a sense of altruism, (3) shared decision-making and right to dissent, (4) notions of integrity, privacy, and access, and (5) understanding of disease risk and personal responsibilities. We conclude that the children feel positive towards medical research, and want to take an active part in decisions and have their integrity respected. However, the study also indicates that children who had participated in longitudinal screening had a limited understanding, suggesting the vital importance of providing information appropriate to their age and maturity. This information should be provided out of respect for the children as persons, but also to promote their willingness to continue participating in longitudinal studies.