This study investigates the perceptions of Malaysian undergraduates of the Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM) towards an online English for science and technology course in terms of their improvement in reading skills and strategies, their autonomy and their motivation. These three areas were used as the focal points in the study as they are educational qualities that are closely interrelated and mutually reinforcing. The research study was a case study incorporating quantitative and qualitative research methods. The data required were gathered in three phases, with phase one being implemented when the students were in the first semester. The methods applied in this phase for gathering data on the perception of the students were: (i) monitoring logging-in days and times; (ii) initiating online discussion via an online forum and; (iii) administrating online questionnaires. Phase two of the study was implemented at the end of the first semester, after the students finished the course. Semi-structured interviews were conducted to gather data for this phase. The third phase was implemented when the students were in their final year. This time in-depth interviews were conducted. The data were collected, categorised, analysed and discussed in line with the three focal points of the study. The findings of the three phases of the study revealed that the students perceived this course as contributing highly towards their improvements in reading skills and strategies, contributing moderately towards improving their autonomy as some of them did not desire full autonomy in that they still indicated a preference for a combination of both face-to-face and online modes of learning and contributing highly towards their motivation. (Contains 4 tables and 2 figures.)