Based on conceptual change theory, cognitive conflict is known as an important factor in conceptual change even though there are still questions about its positive and negative effects on science learning. However, there is no reliable method by which to assess the cognitive conflict students experience in their learning. The purpose of this research was to develop an instrument for measuring secondary students' cognitive conflict levels as they learned science. The results of this study indicate that our instrument is a valid and reliable tool for measuring cognitive conflict levels. Factor analysis supported the model that cognitive conflict consists of four constructs: recognition of an anomalous situation, interest, anxiety, and cognitive reappraisal of the conflict situation. Implications for instruction and possibilities for future research are discussed. © 2003 Wiley Periodicals, Inc. J Res Sci Teach 40: 585–603, 2003