This study examined the associations of parents’ expressed emotion (EE) and parenting stress, with behavioral problems of children with 22q11.2 deletion syndrome, idiopathic autism (iASD) and typically developing (TD) children. Parents of children aged 3–8 years completed the five-minute-speech-sample (FMSS), parental stress index and children behavioral checklist. Parents’ FMSS-EE-criticism was higher among parents of children with 22q11DS and iASD compared to parents of TD children. FMSS-EE scores predicted children's behavioral problems, above and beyond parenting stress. The associations between FMSS-EE, parenting stress and children’s behavioral problems were consistent across 22q11DS, iASD and TD children. These findings highlight the need for targeting parents’ EE and parenting stress as integral elements in the screening and prevention of behavioral problems of young children with 22q11DS and iASD.