Maternal substance use has been associated with a range of child risk factors. The study investigated the relationship between engagement with child health services and child protection outcomes for children of substance-using mothers. The sample comprised 119 children of mothers who disclosed opiate, amphetamine or methadone use during a maternity admission between 2000 and 2003. Statutory child protection agency and child health engagement information for the first 2 years of life was obtained. The relationship between type of maternal substance use, child health engagement and child protection outcomes was examined. Of study group infants, 72% were engaged with child health services during the first 2 years of life. Chi-squared analysis showed no significant relationship between child health engagement and child protection reports. Child health engagement was associated with decreased substantiated child protection notifications for children of methadone using mothers, but not for children of illicit substance users. Almost a quarter of identified children of substance-using mothers are not accessing standard child health services in their first 2 years of life. This study provides support for increased attention to the provision of child health services for children of methadone using mothers. Further research into effective intervention strategies for children of illicit substance-using mothers is indicated.