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In Australia, non-government schools consistently outperform government schools in standardized tests of literacy and numeracy. However, student heterogeneity across school sectors suggests that this performance differential may not be entirely attributable to the nature of the schools. This study investigates the extent of non-government school advantage, after controlling for characteristics of students and their families. We focus on primary schools, where the foundation for later learning is laid. Test scores, from the National Assessment Program Literacy and Numeracy, of a nationally representative sample from the Longitudinal Study of Australian Children are analysed using econometric methods that take account of the complex nature of the sample design. We find little evidence that attendance at non-government primary schools has a positive effect on academic outcomes. Our findings challenge common perceptions of non-government school efficiency and raise some important questions about current policies for funding Australian primary schools.