Background: Self-injurious behaviour is frequently identified as part of the behavioural phenotype of Cornelia de Lange syndrome (CdLS). We conducted a case-control study of the prevalence and phenomenology of self-injurious behaviour (SIB) in CdLS. Methods: A total of 54 participants with CdLS were compared with 46 individuals who were comparable on key variables including age, degree of intellectual disability and wheelchair use, using questionnaire and observational measures. Results: Clinically significant self-injury was not more prevalent in the CdLS group (55.6%), nor was it different in presentation from that seen in the comparison group. Hyperactivity, stereotyped and compulsive behaviours predicted clinically significant self-injury in all participants. Hand directed, mild self-injury was more prevalent in CdLS. Conclusions: The results show that clinically significant self-injury may not be part of the behavioural phenotype of CdLS but a specific body target for proto-SIB is more common.