Poor physical health and behavioural and emotional problems in childhood have a lasting impact on well-being in adolescence and adulthood. Here we address the relationship between poor parent and child physical and mental health in early childhood (age 5) and conduct, hyperactivity and emotional problems in mid-childhood (age 10/11). We compare results across two generations of British children born 30 years apart in 1970 (n = 15,856) and 2000/2 (16,628). We take advantage of rich longitudinal birth cohort data and establish that a child’s own poor health was associated with conduct, hyperactivity and emotional problems in mid-childhood in both generations, and that with the exception of conduct problems in the 1970 cohort these relationships remained when family socio-economic status and individual characteristics were accounted for. Poor maternal mental health was similarly associated with conduct, hyperactivity and emotional problems in both generations; poor parental physical health with a child having later hyperactivity and emotional problems in the younger generation. Results also indicated that earlier behaviour problems had more influence on later problems for children in the more recent cohort. Given the increasing proportion of children and adolescents with mental health problems and that socio-economic disadvantage increases physical and mental well-being concerns within families, policy solutions must consider the holistic nature of a child’s family environment to prevent some children experiencing a ‘double whammy’ of disadvantage. The early years provide the best opportunity to promote children’s resilience and well-being and minimise the development of entrenched negative behaviours and their subsequent costs to society.