Objective To study the effects of group B Streptococcus (GBS) colonization in late pregnancies on neonatal GBS infection. Methods A total of 17 019 pregnant women who received antenatal care and delivered in Xiamen Maternal and Child Care Hospital from June 1, 2014 to May 31, 2015 were enrolled in this study. Secretions from the lower third of the vagina in the pregnant women at 35-37 weeks of gestation or having premature baby(regardless of gestational age) were obtained to test GBS by standard bacterial culture, and 1 472 cases underwent GBS DNA test by real-time fluorescent quantitative-polymerase chain reaction (PCR) meanwhile. The pregnant women colonized with GBS (GBS culture and/or PCR DNA test positive) were given intrapartum antibiotic prophylaxis (IAP) during parturition or rupture of fetal membranes. Detection rate of the two methods was compared, and the effects of GBS colonization and IAP on neonatal GBS infection were analyzed to identify the risk factors of neonatal early-onset GBS disease (GBS-EOD). Two independent samples t-test, Chi-square test and Logistic regression analysis were used for statistical analysis. Results The detection rate of GBS culture and PCR DNA test was 14.43% (2 456/17 019) and 14.13%(288/1 472), respectively. The total colonization rate was 14.52%(2 472/17 019). Based on the culture results as golden criteria, the sensitivity, specificity, positive predictive value and negative predictive value of PCR assay were 95.05%, 98.74%, 92.31% and 99.21%, respectively. There were 17 332 deliveries from the 17 019 pregnant women, of which 31 cases had GBS-EOD. The incidence of neonatal GBS-EOD in maternal GBS colonization [1.05%(26/2 472)] was 31 times higher than in pregnant women without GBS colonization [0.34‰(5/14 547)]. Among the 31 infants with GBS-EOD, 24 had pneumonia, five had sepsis, and two had meningitis. The case fatality rate was 6.45%(2/31). Logistic regression analysis found that chorioamnionitis was an independent risk factor of neonatal GBS-EOD (OR=40.425, 95%CI: 7.514-379.782, P=0.000). Compared with the non-IAP group,IAP group had a lower incidence of GBS-EOD among the pregnant women colonized with GBS [0.94%(23/2 443) vs 10.34%(3/29), χ2=24.350, P<0.01]. Conclusions GBS colonization in late pregnant women has adverse effects. Therefore, routine maternal rectovaginal culture of GBS may be necessary and IAP should be applied in those with GBS colonization. Key words: Pregnancy trimester, third; Vagina; Streptococcus agalactiae; Streptococcal infections; Infant, newborn