In this study, a multimedia e-book system is built and its use monitored in an empirical study investigating various factors which effect learners' reading preferences. 69 fifth-grade students participated in this experiment, one student with an attention deficit hyperactivity disorder was excluded. After three weeks of learning activities, we found that there are differences in browsing patterns, navigation facilities, and annotation patterns in terms of gender. In the cognitive style, holists use bookmarks (tags made by the learner) to navigate more than serialists. Also, regarding annotation patterns, there are statistically significant differences related to the degree of the user's prior knowledge. Parts of the results are similar to those found in previous research, as well as some interesting findings. The findings of this study contribute a deeper understanding of the relationship between human factors and the usage of e-books. This understanding can be applied to develop adaptive e-books that can accommodate learners' individual differences.