Self-paced reading and eye-tracking can be used to measure microlevel student engagement during science instruction. These methods imply a definition of engagement as the quantity and quality of mental resources directed at an object and the emotions and behaviors entailed. This definition is theoretically supported by models of reading comprehension and visualization comprehension. The use of eye-movement data is based on a number of assumptions, including the assumption that people look longer at words and images because they are thinking about those objects more. Self-paced reading and eye-tracking have strengths such as precision and detail as well as limitations including difficulty of interpretation. Carefully controlled research designs and triangulation of multiple methods are suggested as possible ways to address the limitations and take advantage of the strengths. Two examples drawn from the refutational text literature are described.