Background. Because classic pneumococcal serotyping methods cannot distinguish between serotypes 6A and 6C, the effects of pneumococcal vaccines against serotype 6C are unknown. Pneumococcal vaccines contain serotype 6B but not serotypes 6A and 6C. Methods. We used a phagocytic killing assay to estimate the immunogenicity of the 7-valent conjugate vaccine (PCV7) in children and the 23-valent polysaccharide vaccine (PPV23) in adults against serotypes 6A and 6C. We evaluated trends in invasive pneumococcal disease (IPD) caused by serotypes 6A and 6C in the United States, using active surveillance. Results. Serum specimens from PCV7-immunized children had median opsonization indices of 150 and <20 for serotypes 6A and 6C, respectively. Similarly, only 52% of adults (25 of 48) vaccinated with PPV23 showed opsonic indices of>20 against serotype 6C. During 1999-2006, the incidence of serotype 6A IPD decreased by 91% (from 4.9 to 0.46 cases per 100,000 persons; P < .05) among individuals aged <5 years and by 58% (from 0.86 to 0.36 cases per 100,000 persons; P < .05) among those aged ≥5 years. Although the incidence of 6C IPD showed no consistent trend (range, 0-0.6 cases per 100,000 persons) among individuals aged <5 years, it increased from 0.25 to 0.62 cases per 100,000 persons (P < .05) among those aged ≥5 years. Conclusions. PCV7 introduction has led to reductions in serotype 6A IPD but not serotype 6C IPD in the United States. © 2008 by the Infectious Diseases Society of America. All rights reserved.