The Reaction Coordinate Diagram Inventory (RCDI) was developed to measure chemistry students' thinking and confidence when interpreting the kinetic and thermodynamic information encoded within reaction coordinate diagrams (RCDs). The RCDI was designed based upon analyses of qualitative data collected in semi-structured interviews with general chemistry students or organic chemistry students to ensure all items and distractors were grounded in students' ideas and reasoning. A longitudinal, multi-institution research study was conducted using the RCDI to measure changes in undergraduate chemistry students' reasoning with RCDs, and their confidence in doing so, at three points in time: (1) end of second-semester general chemistry, (2) beginning of first-semester organic chemistry, and (3) end of first-semester organic chemistry. The three institutions participating in this longitudinal study taught organic chemistry using either a traditional functional group curriculum or a mechanisms approach. Findings include evidence that individual students performed significantly better with significantly higher confidence as they progressed through courses, but that some RCD misconceptions, such as incorrectly assuming reaction progress indicates a time unit, are persistent throughout. Although two of the institutions taught organic chemistry using a mechanisms curriculum and one institution used the traditional functional group approach, no evidence exists of significant differences among students' RCDI total score and average confidence across institutions.