The ability to read English efficiently and effectively is important for medical students because they have to read a lot of medical texts published in English. This is challenging especially for non-native speakers. This study measures Taiwanese medical students' self-perceived use of metacognitive strategies while reading printed texts and hypertexts, and also the potential impact of hypertext on English reading comprehension. The results of the study showed that the strategies used the most by the printed text and hypertext groups were problem-solving strategies, followed by global strategies; whereas support strategies were least used. Learners in the printed text group reported more strategy use of reading slowly and using background information than the learners in the hypertext environment. A significant reading improvement and positive correlations were found between the strategies of guessing content, checking guesses, and guessing unknown words on hypertext comprehension enhancement. Such results suggested that the majority of students frequently used the three specific strategies and the degree of such strategy uses was reliably predicted by their comprehension scores. Based on the investigation results, limitations and future research are discussed and presented.