Streptococcus agalactiae (Group B streptococcus, GBS) is the most important pathogen causing neonatal sepsis. The role of bacterial proteins contributing to pathogenicity in GBS infections has not yet been clearly determined, but the C protein complex has been suggested to be involved in both virulence and protective immunity. The aim of this study was to assess the prevalence of GBS strains bearing the gene encoding for the beta antigen of the C protein among clinical isolates from 68 neonates with sepsis, 45 newborns colonized without clinical signs of infection, and 50 isolates from pregnant women. The prevalence of the beta antigen gene in all three groups was low (24% vs. 19% vs. 22%) [corrected], and the differences between groups were not statistically significant. Clinical characteristics and cytokine plasma levels did not differ between septic patients with beta antigen-positive and -negative strains. The beta-antigen gene was not found among serotype III isolates, which accounted for roughly half of all the strains isolated. Thus, polymerase chain reaction (PCR) analysis based on the beta antigen gene seems not helpful for distinguishing invasive from colonizing GBS strains. A vaccine based on peptide antigens from the beta antigen of the C protein would most probably not provide protection against the majority of GBS isolates. When analyzing the PCR products of the C protein beta antigen gene by DNA sequencing, a genetic heterogeneity was observed, revealing small repetitive genetic elements within the amplified fragment, an observation that should be studied further.