In this paper we draw on the hypothesis of “Effectively Maintained Inequality” (EMI), which holds that inequalities in higher education concern differentiation as regards the institutions or study programmes which people from different socioeconomic backgrounds choose, rather than the difference between participating and non-participating. It is an important issue, as in modern knowledge and information societies, characterized by new methods of getting, processing and distributing information, higher education is important as a means of equipping people with the knowledge necessary to participate actively in them, for personal growth and national growth. It also impacts positively on social justice, equality of educational opportunity and can boost intergenerational social mobility. These potential benefits, however, are undermined by segregation within higher education. In this paper we present the findings of a research study that examined the breadth of segregation of the higher sector in Greece by socioeconomic background. Research findings indicate a correlation among cultural, social and financial capital and programme or institution, thus conforming the theory of “Effectively Maintained Inequality”.