Genotyping of human rotaviruses was performed in 191 rotavirus-positive fecal samples collected from infants with acute gastroenteritis, 3 years after the introduction of two rotavirus vaccines in South Korea. Among these samples, the most prevalent rotavirus genotype was G3P (30.9%), followed by G1P (27.7%), G4P (15.2%), and G9P (5.8%). Sequence analysis identified RotaTeq® vaccine-derived strains in 12 samples (6.3%), comprising 11 G1P human–bovine double reassortant rotaviruses and 1 G1P human–bovine single reassortant rotavirus. It is of note that cross-reactivity between the current G4-specific typing primer and RotaTeq®-specific G1 genotypes was found. A trace of the clinical and environmental routes of the rotavirus vaccine strains revealed unexpected complexity, and the diagnostic protocol for rotaviruses may require modification by using either another typing primer set or nucleotide sequence analysis. J. Med. Virol. 87: 112–116, 2015. © 2014 Wiley Periodicals, Inc.