Who should decide a scientist’s research agenda? The scientist him- or herself? Superiors, such as science ministries or university management? Sponsors, such as funding organizations or industry? Interest groups, such as churches, political parties, animal rights organizations or patient initiatives? What is the right balance between the scientist’s autonomous decision on the one hand and players’ interests on the other? These questions will not be answered here, but reflected upon with regard to the difficult trade-offs involved and the threats to scientific freedom that can result from them. For this purpose, I propose an analytical framework that conceptualizes the thematic autonomy of science as a gradual interplay of individual choices of research topics made in the context of the respective scientific community, on the one hand, and external constraints, on the other. With regard to them, seven basic levers will be distinguished. This framework will be applied to the current state of German professors’ freedom to choose their research agenda.