Using self-determination theory (SDT) as a conceptual framework, this research examines motivation in our nation's science classrooms by conducting a secondary data analysis of the High School Longitudinal Study of 2009 (HSLS:09). The study describes the creation of a valid measure of autonomy support within HSLS:09 and validates critical components of SDT with a nationally representative sample of data. Results indicate males and females do not differ meaningfully on measures of autonomy support, science perceived competence, science interest, or science identity. Autonomy support was a statistically significant predictor of science perceived competence, science interest and science identity, and these relationships were the same for males and females. Among US ninth-graders intending to pursue STEM occupations, 84% are boys and 16% are girls. Science perceived competence and science identity mediated the relationship between science autonomy support and students' intentions to pursue a STEM career. Additionally, science perceived competence and science identity significantly discriminated between students who intended to pursue a STEM occupation and those who did not.