Background: Longitudinal research is needed to strengthen evidence for risk factors for challenging behaviour in children with intellectual disabilities and to understand patterns of change over time. Methods: Data on challenging behaviour were collected for 225 students in one school over four annual time points and a range of potential risk correlates. Data were analysed using Generalised Estimating Equations. Results: Prevalence of challenging behaviour, aggression and self-injury did not vary significantly over time. Stereotyped behaviours increased over the 4-year period. Challenging behaviour was associated with lower levels of adaptive skills and autism. Stereotyped behaviour increased with age. Self-injurious behaviour was less likely to be shown in children with profound intellectual disabilities over time. Conclusions: These findings are consistent with previous research in terms of potential risk factors identified. Implications for schools include proactive interventions for children with intellectual disabilities at high risk; especially those with autism and poorer adaptive skills.