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Adolescents face many barriers on the path towards a STEM profession, especially girls. We examine the gender stereotypes, cognitive abilities, self-perceived ability and intrinsic values of 546 Russian school children from 12 to 17 years old by sex and STEM preferences. In our sample, STEM students compared to no-STEM have higher cognitive abilities, intrinsic motivation towards math and science, are more confident in their math abilities and perceive math as being easier. Boys scored higher in science, math and overall academic self-efficacy, intrinsic learning motivation and math’s importance for future careers. Meanwhile, girls displayed higher levels of gender stereotypes related to STEM and lower self-efficacy in math. A network analysis was conducted to identify the structure of psychological traits and the position of the stem-related stereotypes among them. The analysis arrived at substantially different results when adolescents were grouped by sex or preference towards STEM. It also demonstrated that gender stereotypes are connected with cognitive abilities, with a stronger link in the no-STEM group. Such stereotypes play a more important role for girls than boys and, jointly with the general self-efficacy of cognitive and academic abilities, are associated with the factors that distinguish groups of adolescents in their future careers.