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Students' thinking patterns in learning organic chemistry were tracked through the one-year course taught to a total of approximately 1300 students, mostly biology majors, for a period of 2 years. As expected, the students' knowledge base increases, but the cognitive organization of the knowledge is surprisingly weak and misconceptions persist even after two years of college chemistry. Both a simple analysis of percentage of correct responses on pretests and posttests and establishing the connectivity of these responses by using the "knowledge space theory" (KST) were applied. Student responses were used to determine the students' knowledge structure and their critical learning pathway, which reflect the cognitive organization of their knowledge. Electron density distribution in the molecule was used as the organizing principle. The results indicate that the organizational structure for organic chemistry, whether it is based on electron density, functional groups, or other organizing principles, needs to become even more transparent for students to make it a part of their own construction of knowledge. The KST analysis provides a new way to assess students' cognitive organization of knowledge and has therefore enabled us to teach with greater insight.

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