Abnormal breathing control is linked to several disorders such as sleep apnoea, panic attack, and sudden infant death. This study investigated the development and functioning of breathing control. Previous studies found that a small part of the brain, the preBötzinger Complex, is responsible for the generation of automatic, rhythmic breathing. The preBötzinger Complex is still developing during the first few days after birth, making this period extremely vulnerable to drugs. One of the first painkillers offered to mothers during child-birth is an opioid painkiller known as fentanyl, but its effects on new-borns are not entirely understood. Previous research shows that fentanyl can cross the placenta and it can be secreted into breast-milk. In this study, new-born mice were injected with fentanyl to test its long-term effects on breathing. These animals were also injected with fentanyl during adulthood to test whether they respond to the painkiller differently to those animals that have never been exposed. The fentanyl pre-exposed mice showed a decreased baseline breathing, an altered response to fentanyl during adulthood, and increased number of sighs, hiccups, apnoea and hyperpnoea. Further findings showed increased weight and abnormal stress-related behaviour in these mice. These results suggest that fentanyl exposure can have long-term effects on new-borns. The findings of the present study raise the question of the safety of maternal fentanyl use during pregnancy, labour and breastfeeding.