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Internal exclusion (aka isolation) is the temporary relocation of a pupil from their classroom to a designated isolation space as a consequence of disruptive behaviour. Secondary analysis of a large cohort dataset (k = 121 mainstream secondary schools; N = 34,377) revealed that 8.3% of pupils reported being internally excluded at least once a week. Multiple marginalised/othered groups (e.g., special educational needs; minoritised ethnic groups; LGBTQ+) were disproportionately internally excluded. Propensity-score-weighted analysis revealed that isolation negatively impacts school belonging (d=-0.15) and relationships with school staff (d=-0.18), with additional subgroup effects for girls’ mental wellbeing (d=-0.07). We conclude that isolation is a very widely used but discriminatory and harmful practice; accordingly, alternative behaviour management approaches are needed.