A central tenet of self-regulated learning theories is that students are motivated towards learning in order to self-regulate. It is thus important to identify student motivations in order to inform efforts to improve instructional strategies that encourage self-regulation. Here we describe a study aimed at characterizing the important motivation factors for students taking general organic chemistry, and how they connect to, and correlate with student performance. A cross-sectional study was conducted involving 2648 undergraduate student participants at two institutions over five semesters and four instructors. Motivation was measured using the Organic Chemistry Motivation Survey (OCMS), a modified form of Glynn et al. (2011)'s Science Motivation Questionnaire II (SMQ-II). The results suggest that the students were highly motivated towards earning a high grade, but that this grade motivation correlated only weakly with performance. Other intrinsic and extrinsic motivation factors were found to be low, suggesting that the students perceived organic chemistry to have little relevance to their interests and careers. However, student performance was strongly correlated with self-efficacy, and, to a lesser extent, self-determination. This finding implies that high-performing students tended to be self-regulated learners who are not motivated primarily by the relevance of the course content. Alternate sources of motivation that can drive self-regulation are discussed.