Students' academic self-concept is a good predictor of academic achievement and a desirable educational outcome per se. In this study, we take a closer look at the nature of the academic self-concept in the natural sciences by examining its dimensional structure, its relation to achievement, and gender differences. We analyzed data from self-concept measures, grades and standardized achievement tests of 6036 German 10th graders across three science subjects – biology, chemistry, and physics – using structural equation modeling. Results indicate that (a) a 3-dimensional, subject-specific measurement model of the self-concept in science is preferable to a 1-dimensional model, (b) the relations between the self-concept and achievement are substantial and subject-specific when grades are used as achievement indicators, and (c) female students possess a lower self-concept in chemistry and physics even after controlling for achievement measures. Therefore, we recommend conceptualizing the self-concept in science as a multidimensional, subject-specific construct both in educational research and in science classes.