Access into higher education has traditionally been dominated by males. However, the current situation in Malaysia as well as in many developed and developing nations is that females have outnumbered males in higher education. By comparing gender enrolment, this paper illustrates the extent of gender disparity in Malaysian higher education across different higher education institutions, levels of study and fields of study. The disparity across the three dimensions can be summarised as a trend in which there is over-representation of females in public universities, in all disciplines except engineering, manufacturing and construction, and at all levels except the doctorate. Importantly, although set in Malaysia, this paper has wider implications where the trend of gender disparity underlined two areas of concern, namely an overly emphasised academic admission for transition from schools into higher education and the differentiated willingness of households to spend on higher education for their sons and daughters.