We present an eye tracking study to investigate how natural reading behavior and reading comprehension are influenced by in-context annotations. In a lab experiment, three groups of participants were asked to read a text and answer comprehension questions: a control group without taking annotations, a second group reading and taking annotations, and a third group reading a peer-annotated version of the same text. A self-made head-mounted eye tracking system was specifically designed for this experiment, in order to study how learners read and quickly re-read annotated paper texts, in low constrained experimental conditions. In the analysis, we measured the phenomenon of annotation-induced overt attention shifts in reading, and found that: (1) the reader's attention shifts toward a margin annotation more often when the annotation lies in the early peripheral vision, and (2) the number of attention shifts, between two different types of information units, is positively related to comprehension performance in quick re-reading. These results can be translated into potential criteria for knowledge assessment systems.