Background: In recent times the basic understanding, perceptions and CAM use among undergraduate health sciences students have become a topic of interest. This study was aimed to investigate the understanding, perceptions and self-use of CAM among pharmacy students in Malaysia.Methods: This cross-sectional study was conducted on 500 systematically sampled pharmacy students from two private and one public university. A validated, self-administered questionnaire comprised of seven sections was used to gather the data. A systematic sampling was applied to recruit the students. Both descriptive and inferential statistics were applied using SPSS® version 18.Results: Overall, the students tend to disagree that complementary therapies (CM) are a threat to public health (mean score = 3.6) and agreed that CMs include ideas and methods from which conventional medicine could benefit (mean score = 4.7). More than half (57.8%) of the participants were currently using CAM while 77.6% had used it previously. Among the current CAM modalities used by the students, CM (21.9%) was found to be the most frequently used CAM followed by Traditional Chinese Medicine (TCM) (21%). Most of the students (74.8%) believed that lack of scientific evidence is one of the most important barriers obstructing them to use CAM. More than half of the students perceived TCM (62.8%) and music therapy (53.8%) to be effective. Majority of them (69.3%) asserted that CAM knowledge is necessary to be a well-rounded professional.Conclusions: This study reveals a high-percentage of pharmacy students who were using or had previously used at least one type of CAM. Students of higher professional years tend to agree that CMs include ideas and methods from which conventional medicine could benefit.