Investigations of sex differences in the human brain take place on politically sensitive terrain. While some scholars express concern that gendered biases and stereotypes remain embedded in scientific research, others are alarmed about the politicization of science. This talk sets out three kinds of conflicts that can arise in the neuroscience of sex differences: academic freedom versus gender equality; frameworks, background assumptions, and dominant methodologies; and inductive risk and social values. The boundaries between fair criticism and politicization are explored for each kind of conflict, pointing to ways in which the academic community can facilitate fair criticism while protecting against politicization.