A total of 52 clinical isolates of group B streptococci (GBS) was tested for expression of the c protein c(alpha) by a fluorescent antibody test (FAT) and by PCR amplification of a 202-bp stretch within the repeat unit of the bca gene encoding the c(alpha) protein. The strains were categorised as follows: c(alpha) FAT positive and PCR positive with amplification products of multiple sizes (category A, n = 12); FAT negative and with PCR products of multiple sizes (category B, n = 11); FAT negative and with a single PCR product of c. 200 bp (category C, n = 5); negative in both tests (category D, n = 24). A single amplification product of minimum size and additional products of larger sizes corresponded to one and more bca repeats, respectively. Five of the 11 category B strains showed expression of low Mr c(alpha) in whole cell-based Western blotting. The results showed that a proportion of the GBS isolates harboured bca gene elements that either were not expressed or they expressed c(alpha) molecular variants which could not be detected by the whole cell-based FAT. This genotype/phenotype discrepancy should be considered in relation to GBS typing, including the selection of antibody reagents and the technical approach to c(alpha) protein detection.