Secondary school differentiation in Australia is a substantial driver of the segregation of low SES and Indigenous students. Such segregation acts as a mechanism for the intergenerational transfer of social disadvantages. Indigenous students are doubly-segregated into schools with high concentrations of low SES and Indigenous students. No school type is representative of the student population. Catholic, independent and public selective schools are associated with student segregation within geographical areas. School fees are the strongest predictor of segregation and partially explain the effect of differential school types. Independent schools are the strongest school type predicting segregation, followed by Catholic, then selective schools. States with lower rates of Catholic, independent and selective schools have lower levels of segregation. Private schools are far from enrolling a fair proportion of disadvantaged students in proportion to the public financing they receive. Substantial reforms to school and system reporting are required to end the exclusion of disadvantaged students.