This study first explores intermediate-level English learners' preferences for hypermedia annotations while they are engaged in reading a hypermedia text. Second, it examines whether multimedia annotations facilitate reading comprehension in the second language. The participants were 44 adult learners of English as a foreign language studying English for Academic Purposes. Data were collected through a tracking tool, a reading comprehension test, a questionnaire, and interviews. Results indicate that learners preferred visual annotations significantly more than textual and audio annotations. On the other hand, a negative relationship was found between annotation use and reading comprehension. Especially, pronunciations, audiorecordings, and videos were found to affect reading comprehension negatively. However, the qualitative data revealed that the participants had positive attitudes towards annotations and hypermedia reading in general.