The molecular mechanism of pneumococcal vaccine failure in human immunodeficiency virus (HIV)-infected persons is not fully understood. A polymerase chain reaction ELISA was used to determine the proportion of peripheral IgG, IgA, and IgM CD19-positive B cells expressing 6 immunoglobulin heavy-chain variable region (VH) subgroups before and 7 days after pneumococcal vaccination of 12 HIV-infected and 12 HIV-uninfected subjects. Significant postvaccination increases in the expression of the VH3 subgroup by IgG and IgA and a greater serologic response to vaccination were observed in the HIV-uninfected group. In contrast, the HIV-infected group had reduced prevaccination IgG VH3 and a postvaccination increase in IgG VH5. These results demonstrate that pneumococcal vaccination changes the pattern of B cell VH gene expression and support the concept that aberrant VH3 expression may translate into a poor antipneumococcal response in the setting of HIV infection.