Background: The administration of intrapartum antibiotics prophylaxis (IAP) is commonly used for the prevention of early-onset Group-B-streptococci (GBS) infection. IAP may influence the oral microbiome in neonates. Our study aimed to compare the oral bacteriome between neonates grouped according to their exposure to antibiotics during the delivery and sampling time in the first week of their life. Methods: In this case-control study, oral samples were collected from healthy neonates (n=66) from the CELSPAC:TNG cohort during their hospital stay. The neonates were classified into the group of those delivered by C-section or vaginally with IAP (n=33) and the control group of neonates delivered vaginally without IAP (n=33). The bacteriome profile was determined by 16S rDNA sequencing based on the V3-V4 hyper-variable region. The effect of IAP was tested separately for samples collected within 48 hours of delivery and for those collected later.   Results: Differences in alpha diversity (Shannon index, p=0.01) and bacterial composition (p=0.04, PERMANOVA) were observed in oral samples collected within 48 hours after birth, while bacteriomes in oral samples collected later were similar between IAP and control groups. The genera Streptococcus, Gemella, and Rothia dominated in the oral samples in all groups. Of individual genera, only the relative abundance of Gemella was significantly lower in samples collected within 48 hours after birth in neonates compared to the IAP group (q=0.08). Conclusion: Our results illustrate the effect of IAP on oral bacteriome of neonates within the 48 hours after birth. However, this effect seems to be suppressed during the first week of their life.