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This study integrated eye-tracking technology to investigate in depth the effects in animation-based learning environments of utilizing visual cuing techniques on learners’ understanding of lesson content and on learners’ information processing efficiency. Thirty-two college students participated in this study. The participants were randomly assigned in to either cued or non-cued animation group. The results showed a visual cuing effect on student learning with computer animations. The eye-tracking data showed, however, the effect seemed to be affected by the sequence, size, and movements of the components in the computer animations. Future studies are suggested to investigate if visual cuing techniques interact with the size, movements, and shape of the animated components on affecting viewers’ visual searching efficiency.