Studies comparing the immunogenicity and reactogenicity of trivalent inactivated subunit (SU) and split (SPL) vaccines in children in Asia are limited. In 2008, we assessed the safety and immunogenicity of SU and SPL influenza vaccines in Korean children aged 6-35 months. We studied 2 non-randomized cohorts of children who received either SU or SPL vaccine in an open-label non-stratified controlled trial at 6 hospitals in Korea. We measured antibody titers with a hemagglutination-inhibition assay at baseline and 30 days after the first or second flu shot. The primary goal was the determination of vaccine immunogenicity according to the European Union Committee of Human Medicinal Products licensing criteria. Out of a total of 106 participants aged 6-35 months, 47 received the SPL vaccine and 59 the SU vaccine. After vaccination, 41 (87.2%), 40 (85.1%), and 33 (70.2%) of the 47 subjects in the SPL group had titers ≥ 1:40 against H1N1, H3N2, and B, respectively. In the SU group, 42 (71.2%), 34 (57.6%), and 22 (37.3%) of 59 subjects had titers ≥ 1:40 against H1N1, H3N2, and B, respectively. The post-vaccination geometric mean titers of H1N1, H3N2, and B (SPL vs SU) were 119.1, 99.8, and 61.4 vs 75.4, 51.2, and 24.1, respectively. There were no serious vaccine-related adverse events. There were no differences between the SPL and SU vaccines with respect to adverse events. The immunogenicity of the SPL vaccine appears to be better than that of the SU vaccine in children aged 6-35 months in Korea.