Objective: To gain insight into pregnant women's preferences if given a choice between getting antibiotic prophylaxis before or after cord clamping during caesarean delivery. Study design: A qualitative semi-structured interview-study. The interviews were conducted at a Danish Hospital, with about 4000 deliveries a year. Fourteen individual semi-structured interviews were conducted with pregnant women, either considering or having a planned caesarean section, or scheduled for induction due to post-term gestational age. A systematic text condensation approach was used to analyze the transcribed interviews. Results: Ten of the fourteen women favored antibiotic administration after cord clamping. Despite any adverse effects to the infant's microbiota and increased risk of long-term health outcomes were only hypothetical and the risk reduction in postpartum infections being well documented, they did not want to expose their offspring to antibiotics. Those who preferred antibiotic prophylaxis before cord clamping were concerned, if they would be able to care for the infant in case of a maternal infection. Three of the women preferring antibiotics after cord clamping said they would potentially change preference, if the maternal risk was higher. Most women preferred to be informed of the use of prophylactic antibiotic and that the timing has consequences for trans-placental exposure to the infant. Conclusions: With most of the interviewed women preferring antibiotic administration after cord clamping, we suggest patients should be involved in the decision regarding timing of prophylactic antibiotics before caesarean section.