Prevention strategies by maternal antibiotic use have provided undeniable benefits for neonates regarding early neonatal group B streptococcal infections. But at a time where the evolution of resistance of Gram negative bacteria is of particular concern, it is our duty to reassess prevention strategies with a careful evaluation of their potential impact on Gram negative bacteria in the newborn. We conducted a literature review to define the state of the art of antenatal antibiotic prophylaxis and its bacteriological consequences on the newborn. Prevention strategies of early-onset neonatal group B streptococcal disease with selective intrapartum chemoprophylaxis should not be challenged, even at the cost of a small increase of the incidence of late-onset infections with resistant Gram negative bacteria. However, other indications seem more controversial and the type of antibiotics used is not always based on methodologically well-conducted studies. In these indications the prevention strategies should consider not only the immediate expected benefits, but also the long-term ecological impact by using whenever possible narrow-spectrum antibiotics.