Objectives: To accurately assess the vertical transmission rate of Methicillin-resistant Staphylococcus aureus (MRSA) and its clinical impacts on pregnant mothers and neonates. Design: A prospective observational cohort study. Setting: Japan. Population: 898 pregnant women and their 905 neonates delivered in gestation week > 32+0 at Toyooka Hospital from August 2016 to December 2017. Methods: MRSA was cultured from the nasal and vaginal samples taken from mothers at enrollment and the nasal and umbilical samples taken from neonates immediately after their birth. We examined the vertical transmission rate of MRSA in mother-neonate pairs. We used multivariable logistic regression to identify maternal/neonatal adverse outcomes associated with maternal MRSA colonization. Main outcome measures: The frequency of maternal/neonatal MRSA colonization and adverse outcomes. Results: The prevalence of maternal MRSA colonization was 6.1% (55/898), and that of neonates was 0.8% (8/905). The prevalence of neonatal MRSA was 12.7% (7/55 mother-neonate pairs) in the MRSA-positive mothers, whereas it was only 0.12% (1/843 pairs) in the MRSA-negative mothers (OR: 121, 95% CI: 14.6-1000). When the maternal vaginal-MRSA was positive, the vertical transmission rate was 44.4% (4/9). Skin and soft tissue infections (SSTIs) developed significantly more frequently in neonates born to the MRSA-positive mothers (OR: 7.47, 95% CI: 2.50-22.3). Conclusions: The prevalence of MRSA in pregnant women was approximately 6%. The vertical transmission rate of vaginal MRSA was as high as 44.4%. Maternal MRSA colonization is associated with increased development of neonatal SSTIs via vertical transmission.