Background and Objectives: Little is known about the health of children exposed to opioid pharmacotherapies in utero. This study aims to examine the health of children from birth to 5 years of age, who were exposed to methadone, buprenorphine, or naltrexone with non-exposed children. Methods: Children were identified by linking the treatment records of women treated with one of the three opioid pharmacotherapies with midwife notifications. Live-born children exposed to methadone (n = 198), buprenorphine (n = 122), naltrexone (n = 67) in utero, and neonates not prenatally exposed to opioids (n = 387) born between 2001 and 2011 in Western Australia were included in the study. The children were then linked to state mortality, hospital, emergency department (ED), mental health, cancer, and reportable diseases from birth up to their 5th birthday. Results: Overall rates of hospital admission were elevated in all three treatments as compared with the control children, while rates of ED attendances were only significantly elevated in the methadone (p =.002) and naltrexone (p =.044) exposed children. In terms of both hospital and ED attendances, the differences between the exposed and control children was most apparent in the neonatal period. Rates of mental health out-patient attendances were elevated in buprenorphine-exposed children as compared with the control (p =.005). Discussion and Conclusions: The study provides evidence to suggest a disparity in the health of children exposed to opioid pharmacotherapies in utero compared with non-exposed control children. Scientific Significance: Exposure to opioid pharmacotherapies in utero may influence the health of children beyond the neonatal period. (Am J Addict 2017;26:845–851).