Background Williams syndrome (WS) is a genetic disorder causing intellectual disability. Children with WS often exhibit various kinds of maladaptive behaviours that affect their social functioning. In order to determine whether these behaviours are syndrome-specific, it would be necessary to compare children with WS with children with other syndromes as well as to provide data on the socio-emotional profile in WS from a variety of cultures. The present study investigated the behavioural profile and its relation to maternal stress in Greek young children with WS in comparison with young children with Down syndrome and typically developing (TD) children. Methods Participants were 60 mothers, 20 in each syndrome group and 20 in the control group. The three groups were matched for mental age. The behavioural profile of the participants was investigated through the Child Behaviour Checklist (1.5-5 years) and maternal stress through the Parental Stress Index. Results In accordance with studies in other cultures, it was found that young children with WS received significantly higher rates in emotional problems and anxiety/depression, compared with both children with Down syndrome and TD children. Moreover, mothers of children with WS reported significantly higher scores in the Total Stress index compared with mothers of TD children. However, in contrast with previous studies, only 25% of children with WS fell into the clinical range in the total Child Behavior Checklist score. Conclusion The consistency of the socio-emotional characteristics of children with WS across cultures and developmental stages implies a strong influence of the genetic phenotype. However, Greek mothers avoided to characterize these behaviours as pathological. Implications of these findings for clinical practice are also discussed.