The extent of between-school segregation, or clustering of disadvantaged students within schools, in England varies depending on the indicator of interest. For example, the trend over time for segregation by student poverty differs from those for ethnicity or special educational need. Additionally the causes of the level of segregation for any indicator will be different from the causes of changes in that level over time. This new paper uses data for all state-funded schools in England from 1989 to 2014 to identify the possible determinants of segregation. The results are summarised for England and its economic regions, and presented in more detail for local authority areas. The long-term underlying level of segregation of each indicator appears to be the outcome of structural and local geographic factors. However, the annual changes in segregation for most indicators can be explained most simply by changes in the prevalence of each indicator. For example, the UK policy of inclusion has considerably increased the number of students with statements of special needs in mainstream schools, and this has resulted, intentionally, in less segregation in terms of this indicator. Segregation by poverty varies at least partly with the economic cycle. Some of the explanatory factors, such as the global economy or the prevalence of specific ethnic minority groups, are not directly under policy-makers' control. This means that it is the more malleable factors leading to the underlying levels of poverty segregation that should be addressed by any state wanting a fair and mixed national school system. In England, these controllable factors include the use of proximity to decide contested places at schools, and school diversity as represented by the growth of Academies and Free Schools, and the continued existence of faith-based and selective schools.