On the basis of comparative statistical data and the results of research among doctors of science in Slovenia we find that the governance of science in Slovenia is gender-biased. The data show that women scientists obviously face aggravating circumstances in their progress up the career ladder, that women are also discriminated in their payment for work and that they receive less honour and prizes. At the same time, the research results show that discrimination in the governance of science is not only limited to women. The basic reasons for bias in science are nepotism and affiliation with lobbies and interest groups. We speak of hidden discrimination because discrimination is a cumulative effect of many separate, yet mutually balanced factors that result in an unbalanced proportion of both sexes in the scientific hierarchy and decision-making positions in science.