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In this study, we used eye-tracking methodology for deeper understanding of the refutation text effect on online text comprehension. A refutation text acknowledges the reader's alternative conceptions about a phenomenon, refutes them and presents the correct conceptions. We tested two hypotheses about its facilitation effect: the coherence hypothesis (refutation text is more coherent than standard text, thus facilitating comprehension) and the elaboration hypothesis (refutation text involves deeper processing, thus facilitating comprehension). Forty university students read one refutation text and one non-refutation text about two science topics. Offline data confirmed that refutation text readers recall more scientific facts than non-refutation text readers. Online eye-tracking measures revealed both an increase and a decrease in reading time in response to the refutation statements. Topic-medial text sentences with the correct science facts were fixated for a shorter time when first encountered in the refutation text. Refutation statements, however, increased integrative processing at the end of each text paragraph, as indexed by longer look-back fixation times on topic-final sentences with the science concepts, as well as longer look-back fixation times directed to the refutation statements. These findings support the elaboration hypothesis and are discussed in the light of current accounts of the refutation effect for theory development and educational practice.