One of the greatest concerns in schools today is how teachers can bring together assessment and learning in a way that is meaningful for students' thinking skills, while focusing on content standards. Better understanding of how different types of technology based thinking tools can be used for improving classroom teaching and learning, especially across the most challenging areas of performance, is crucial. Using thinking tools, as forms of graphically and verbally displayed thinking processes, engages students in a variety of higher-level cognitive activities. What does not show up in students' responses is their thinking patterns and processes of understanding. This article describes how concept mapping methodology that is widely used for learning purposes can be adapted to Evidence-Centered Concept Maps (ECCM) in assessing higher-order thinking. ECCM facilitates the analysis that students conduct and requires them to think more deeply about the multifaceted topic being analyzed than they would have without the thinking tool. The author discusses the educational opportunities for using thinking tools in computer-based formative assessment and instruction.