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This study investigates whether structure-guided highlighting enhances middle school students’ comprehension of expository text. One hundred eighty-six seventh graders were randomly assigned to one of four conditions: study-only, traditional highlighting, color-coded highlighting, or highlighting guided by a matrix graphic organizer. Memory and comprehension were measured, and eye-tracking data collected. Only the matrix-guided condition significantly improved comprehension, aligning with predictions from generative learning theory. Neither traditional nor color-coded highlighting produced significant benefits. Eye-movement data showed that longer gaze durations and more paragraph transitions supported comprehension only when structural guidance was provided. In unstructured conditions, similar patterns likely reflected unproductive processing. Findings suggest that highlighting supports learning only when embedded within explicit scaffolds that help students organize and integrate textual information meaningfully.