Background Autism spectrum disorder (ASD) has been identified as a risk marker for self-injurious behaviour. In this study we aimed to describe the prevalence, topography and correlates of self-injury in individuals with ASD in contrast to individuals with Fragile X and Down syndromes and examine person characteristics associated with self-injury across and within these groups. Method Carers of individuals with ASD (n = 149; mean age = 9.98, SD = 4.86), Fragile X syndrome (n = 123; mean age = 15.32, SD = 8.74) and Down syndrome (n = 49; mean age = 15.84, SD = 12.59) completed questionnaires relating to the presence and topography of self-injury. Information was also gathered regarding demographic characteristics, affect, autistic behaviour, hyperactivity, impulsivity and repetitive behaviour. Results Self-injurious behaviour was displayed by 50% of the ASD sample: a significantly higher prevalence than in the Down syndrome group (18.4%) but broadly similar to the prevalence in Fragile X syndrome (54.5%). Self-injury was associated with significantly higher levels of autistic behaviour within the Down and Fragile X syndrome groups. Within the ASD group, the presence of self-injury was associated with significantly higher levels of impulsivity and hyperactivity, negative affect and significantly lower levels of ability and speech. Conclusions Self-injurious behaviour is prevalent in individuals with ASD and the presence of ASD phenomenology increases the risk of self-injury in individuals with known genetic disorders but without a diagnosis of idiopathic autism. Person characteristics associated with self-injury in ASD indicate a role for impaired behavioural inhibition, low levels of ability and negative affect in the development of self-injurious behaviour.