Background  Few studies have investigated parental separation, partnering and re-partnering among population-based cohorts of children at risk of intellectual or developmental disabilities.Methods  Secondary analysis of data extracted from Waves 1–3 of the UK’s Millennium Cohort Study. Information on the residence status of parents at Waves 1, 2 and 3 was available for 10 848 families.Results  Children with early cognitive delay (ECD) were significantly less likely than other children to be living in households with both biological parents or in households where the mother was married at all time points, including at the time of the child’s birth and when children were aged 9 months, 3 years and 5 years. Although families with a child with ECD were more likely than families with a typically developing child to experience changes in both family composition and marital status over the first 5 years of the child’s life, the net effect of these changes in family composition and marital status from the time of the child’s birth to the time the child was 5 years old was similar for both groups of families. The increased levels of family change amongst families with a child with ECD were wholly accounted for by differences in family socio-economic circumstances.Conclusions  More attention needs to be paid to describing and explaining the dynamics of family composition in the early years of children with intellectual and developmental disabilities. ‘Stress reaction’ models attempting to account for rates of parental separation need to incorporate socio-economic factors.