Capsular serotype surveillance of clinical isolates of Streptococcus pneumoniae is essential for evaluation of the potential impact of introducing multivalent capsular serotype-based vaccines in Latin America. Here, a previously described sequential multiplex PCR method was revised for optimal targeting of prevalent serotypes in Latin America. The revised protocol successfully serotyped 139/147 pneumococci (94.6%) from Brazilian children, demonstrating a labour-efficient, accurate method requiring only conventional PCR capability.