We explored the relationship between efficacy against acute otitis media (AOM) and both ELISA anti-polysaccharide IgG geometric mean concentrations (GMCs) and opsonophagocytic (OPA) geometric mean titres (GMTs) following primary and booster vaccination with pneumococcal protein D (Haemophilus influenzae-derived) conjugate vaccine. It was possible to distinguish between the OPA GMTs of low and high efficacy serotypes, however no such distinction was evident for ELISA GMCs. Also, there was a trend towards lower ELISA and OPA serotype-specific responses in subjects who developed AOM compared to controls. We conclude that serotype-specific OPA GMTs are an important endpoint to consider for evaluation of pneumococcal conjugate vaccines with respect to the protective efficacy against AOM (Study ID: 347414/NCT00119743).