As part of long-standing efforts to promote undergraduates' success in science, researchers have investigated the instructional strategies and motivational factors that promote student learning and persistence in science coursework and majors. This study aimed to create a set of brief measures that educators and researchers can use as tools to examine the undergraduate motivational experience in science classes. To identify key motivational processes, we drew on self-determination theory (SDT), which holds that students have fundamental needs--to feel competent, related, and autonomous--that fuel their intrinsic motivation. When educational experiences meet these needs, students engage more energetically and learn more, cumulatively contributing to a positive identity as a scientist. Based on information provided by 1013 students from 8 classes in biology, chemistry, and physics, we constructed conceptually focused and psychometrically sound survey measures of three sets of motivational factors: (1) students' appraisals of their own "competence," "autonomy," and "relatedness"; (2) the quality of students' behavioural and emotional "engagement" in academic work; and (3) students' emerging "identities as scientists," including their "science identity," "purpose in science," and "science career plans." Using an iterative confirmatory process, we tested short item sets for unidimensionality and internal consistency, and then cross-validated them. Tests of measurement invariance showed that scales were generally comparable across disciplines. Most importantly, scales and final course grades showed correlations consistent with predictions from SDT. These measures may provide a window on the student motivational experience for educators, researchers, and interventionists who aim to improve the quality of undergraduate science teaching and learning.