Background: Children with intellectual disability (ID) are at heightened risk for behaviour problems and diagnosed mental disorder. Likewise, mothers of children with ID are more stressed than mothers of typically developing children. Research on behavioural phenotypes suggests that different syndromes of ID may be associated with distinct child behavioural risks and maternal well-being risks. In the present study, maternal reports of child behaviour problems and maternal well-being were examined for syndrome-specific differences. Methods: The present authors studied the early manifestation and continuity of syndrome-specific behaviour problems in 215 preschool children belonging to 5 groups (typically developing, undifferentiated developmental delays, Down syndrome, autism, cerebral palsy) as well as the relation of syndrome group to maternal well-being. Results: At age 3, children with autism and cerebral palsy showed the highest levels of behaviour problems, and children with Down syndrome and typically developing children showed the lowest levels. Mothers of children with autism reported more parenting stress than all other groups. These syndrome-specific patterns of behaviour and maternal stress were stable across ages 3, 4 and 5 years, except for relative increases in behaviour problems and maternal stress in the Down syndrome and cerebral palsy groups. Child syndrome contributed to maternal stress even after accounting for differences in behaviour problems and cognitive level. Conclusions: These results, although based on small syndrome groups, suggest that phenotypic expressions of behaviour problems are manifested as early as age 3. These behavioural differences were paralleled by differences in maternal stress, such that mothers of children with autism are at elevated risk for high stress. In addition, there appear to be other unexamined characteristics of these syndromes, beyond behaviour problems, which also contribute to maternal stress.