BACKGROUND: A 13-valent pneumococcal conjugate vaccine (PCV13) containing 6 additional serotypes not included in the 7-valent PCV has been developed to broaden protection against Streptococcus pneumoniae, which is responsible for over 500,000 deaths annually worldwide in children <5 years of age. This study in Japanese infants evaluated the immunogenicity and safety of PCV13 given subcutaneously, the standard route for infant vaccination in Japan. METHODS: This phase 3, single-arm, open-label study was conducted at 25 sites. Subjects received PCV13 as a 3-dose infant series and a toddler dose. Parents/legal guardians recorded local reactions and systemic events after each vaccination. The proportion of subjects with serotype-specific antipneumococcal polysaccharide immunoglobulin (Ig)G antibody concentrations ≥0.35 µg/mL was calculated before and 1 month after the infant series and toddler dose. RESULTS: A total of 193 subjects enrolled. The proportion of subjects achieving pneumococcal IgG antibody concentrations ≥0.35 µg/mL was ≥97.2% for all 13 pneumococcal serotypes 1 month after the infant series and 98.9-100% after the toddler dose. IgG geometric mean concentrations were 2.57-14.69 µg/mL after the infant series and 2.06-16.33 µg/mL after the toddler dose. IgG geometric mean concentrations increased from pre- to posttoddler dose by ≥2.8-fold, demonstrating a booster effect. Local reactions and fever were generally mild or moderate in severity. CONCLUSIONS: PCV13 was immunogenic for all serotypes and had a favorable safety profile when administered subcutaneously to Japanese infants. PCV13 should offer broader serotype protection than 7-valent PCV in preventing pneumococcal disease in Japanese children.