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Internationally, consensus can be found on the importance of students’ participation in science, technology, engineering, and mathematics (STEM), but women still remain under-represented in STEM-related fields. Current study focuses on gender differences in motivation profiles and examens how these relate to cognitive ability in STEM. This to identify patterns that can help us better understand woman’s under-representation in STEM. Cluster analyses was used on data collected from 755 students in 8th grade STEM-courses to identify motivation profiles. Using multinominal logistic regression analysis we were able to identify patterns in gender, motivation profile and cognitive ability. Although boys and girls do not show significant differences in cognitive ability in STEM, differences in motivation profiles and a possible interaction effect were identified.