BACKGROUND: The introduction of rotavirus vaccines has decreased the prevalence of rotavirus infections and might have changed the distribution of rotavirus genotypes. However, neonates are not eligible for vaccination and, therefore, are at risk for rotavirus infection while in the hospital nursery or neonatal intensive care unit. Our aim was to evaluate the shift of genotypes of group A rotavirus strains among neonates cared for in two geographically distant hospitals in Korea. METHODS: Analysis of rotavirus P and G genotypes was performed for 63 neonates (27 neonates in Seoul and 36 neonates in Busan) admitted to two hospitals between 2011 and 2013. RESULTS: Among the 63 tested neonates less than one month of age, 61 (96.8%) were infected with genotype G4P. CONCLUSION: This study identified G4P as the most frequently isolated genotypes among neonates in Korea; therefore, prevention of the G4P genotype should be considered for neonates.