Individuals with Cornelia de Lange syndrome (CdLS) have been reported to show comparatively high levels of flat and negative affect but there have been no empirical evaluations. In this study, we use an objective measure of facial expression to compare affect in CdLS with that seen in Cri du Chat syndrome (CDC) and a group of individuals with a mixed aetiology of intellectual disabilities (ID). Method: Observations of three groups of 14 children with CdLS, CDC and mixed aetiology of ID were undertaken when a one-to-one interaction was ongoing. Results: There was no significant difference between the groups in the duration of positive, negative or flat affect. However, the CdLS group displayed a significantly lower ratio of positive to negative affect than children in the other groups. Discussion: This difference partially confirms anecdotal observations and could be due to the expression of pain caused by health problems associated with CdLS or neurological expression of the CdLS gene in facial muscles related to expression of positive affect. However, further research is needed to directly test these possible associations.