Introduction: Neonatal sepsis is one of the major causes of mortality and morbidity in neonates. Early onset neonatal sepsis (EONS) is a severe condition with high mortality rate. EONS commonly caused by maternal microorganism before or during the delivery process. Moreover, mother’s genital tract microorganisms also contribute in EONS incidence. Objective: To identify the relationship between the mothers with vaginal pathogenic bacterial colonization and occurs of EONS. Method: A prospective cohort study was conducted in Dr. Wahidin Sudirohusodo hospital and its network hospital from April until August 2015. Samples included inpartu mothers who met the inclusion criteria, and the babies who were followed up for the development of EONS. Results: Out of 90 samples, there were 56 (62.2%) mothers with pathogenic vaginal colonization. The bivariate analyses result showed that there was no significant difference for EONS occurrence in babies born from mother with vaginal bacterial colonization and those who were not (p=0.399). The frequency of newborn from mothers with vaginal pathogenic bacteria colonization who had EONS was 4 (7.1%), while the frequency of newborns from mother without vaginal pathogenic bacteria colonization was 1 (2.9%). There was no significant correlation between the kind of vaginal pathogenic bacteria colonization and EONS incidence (p=0.163). The pathogenic vaginal colonization was dominated by negative gram bacteria (77.97%). Conclusion: There was no correlation between vaginal bacterial colonization and EONS incidence.