The purpose of this study was to investigate the effects of reading printed text and hypertext on EFL learners’ reading comprehension, especially focusing on reading skills, semantic and syntactic differences and automatic performance. When reading printed text, readers start from the top left-hand corner and finish at the bottom right-hand corner. Reading in this way is a linear activity as readers’ eyes go through the text line by line. When reading hypertext, readers can click a hyperlink to find out certain information. When they click the hyperlink, they are taken to a different web page. How does reading hypertext affect EFL learners’ reading comprehension? What are the difficulties they encounter? The participants in this study were ninety-two Taiwanese students studying at two different institutes of technology. They were divided into two groups according to their scores in General English Proficiency Test (GEPT) Simulated Test: Higher Proficiency Learners (HPL) and Lower Proficiency Learners (LPL). The results showed that participants got higher scores in the reading comprehension test, semantic identification test, syntactic identification test, and automatic performance test on paper than they did when reading hypertext. The results suggest that (a) participants transferred the way they read on paper to the way they read on computer screens, (b) text presented as hypertext affected the way participants read, (c) the merits of hypertext, such as colored pictures, abundant information, did not stimulate participants’ motivation, and (d) participants expressed a negative attitude toward reading on hypertext. The major difficulties participants experienced when reading on hypertext were: they experienced eyestrain, they skipped lines, and they could not take notes or underline any words or text on computer screens. Findings and conclusions from this study may serve as implications and suggestions for web designers and for teachers who intend to introduce hypertext in the language classroom. The ultimate purpose was to explore the effectiveness of using printed text and hypertext in language learning and teaching.