Background: People with intellectual disability may be at elevated risk of adverse consequences of substance use. This study outlines the prevalence of, and factors associated with, substance use in young people with and without intellectual disability. Method: Secondary analysis was undertaken of the Next Steps annual panel study, which follows a cohort through adolescence into adulthood and contains self-report data on smoking, alcohol and drug use. Results: Young people with mild to moderate intellectual disabilities were generally less likely to use substances than young people without intellectual disabilities. The pattern of association with socio-demographic factors was mixed. Overall, matching participants on between-group differences in exposure to extraneous risk factors did not impact on between-group differences in substance use. Conclusions: Young people with mild to moderate intellectual disability are less likely to use substances than their non-disabled peers. Prevention and intervention programs need to be adapted for those in this population who do use substances.