Abstract. OBJECTIVE: To determine if changes have occurred in the causative pathogens and/or antibiotic susceptibility profiles in early onset neonatal infections since initiation of group B Streptococcus (GBS) prophylaxis and to determine risk factors for ampicillin/penicillin resistant microorganisms. STUDY DESIGN: Data on 220 infants with positive blood, urine, or cerebrospinal fluid cultures for bacteria or fungi at ≤seven days of age from 1990–2007 were examined and divided into three epochs, based on intrapartum antibiotic prophylactic (IAP) practices. Pathogens and antibiotic resistance were compared among epochs. RESULTS: A significant decrease in the incidence of GBS infections occurred over time, with no change in the incidence of other pathogens or the emergence of antibiotic resistance, including the very low-birthweight population. In regression analysis, ampicillin resistance was associated with male gender (OR 3.096). CONCLUSIONS: No emergence of antibiotic resistant pathogens was found following IAP use. Changing microorganisms and increasing antibiotic resistance found in prior studies are likely multifactorial. Further study is needed to continue to reduce the rates of common early onset pathogens.