Misconceptions are the "the old, the bad, and the ugly" prior knowledge, ideas or conceptions that the learners have that hinder their further learning in science. Several types of misconceptions that undergraduate students hold about reaction coordinate diagrams (from here on we use the term "reaction coordinate diagrams" and "energy diagrams" interchangeably) are described herein. The rationale of 223 students were coded based on their responses to a multiple-choice question on the topic, and interviews (n = 10) were used to delve deeper into the students' knowledge structures. The results of the open coding of the rationale and the interviews were used in developing an instrument which was administered to 57 students. In this paper, we present the assessment instrument and the alternate conceptions that students have regarding energy diagrams that have not been reported in the literature yet. Implications for instructional approaches particular to the energy diagram topic are discussed.