Despite tremendous advances in neuroscience, the topic “brain, sex and gender” remains a matter of misleading interpretations, that go well beyond the bounds of science. In the 19th century, the difference in brain sizes was a major argument to explain the hierarchy between men and women, and was supposed to reflect innate differences in mental capacity. Nowadays, our understanding of the human brain has progressed dramatically with the demonstration of cerebral plasticity. The new brain imaging techniques have revealed the role of the environment in continually re-shaping our brain all along our lifetimes as it goes through new experiences and acquires new knowledge. However, the idea that biology is a major determining factor for cognition and behavioral gender differentiation, is still very much alive. The media are far from being the only guilty party. Some scientific circles actively promote the idea of an innate origin of a gender difference in mental capacities. Experimental data from brain imaging, cognitive tests or genetics are often distorted to serve deterministic ideas. Such abuse of “scientific discourses” have to be counteracted by effective communication of clear and unbiased information to the citizens. This paper presents a critical analysis of selected examples which emphasize sex differences in three fields e.g. skills in language and mathematics, testosterone and financial risk-taking behavior, moral cognition. To shed light on the data and the methods used in some papers, we can now—with today’s knowledge on cerebral plasticity—challenge even more strongly, many false interpretations. Our goal here is double: we want to provide evidence against archaic beliefs about the biological determinism of sex differences but also promote a positive image of scientific research.