The C protein alpha- and beta-antigens are immunodominant components of the surface of Streptococcus agalactiae, the most frequent cause of neonatal sepsis. Both proteins are thought to contribute significantly to virulence of S. agalactiae. They are mainly expressed by serotypes Ia, Ib, and II. The C protein beta-antigen (Cbeta-protein) binds to the Fc portion of human IgA and seems to be of importance in bacterial resistance to mucosal immune defense mechanisms. In this study, PCR analysis of S. agalactiae isolates obtained from 189 neonates and 112 pregnant women revealed the presence of the Cbeta-protein gene in 19% and 22% of the isolates, respectively. Size polymorphisms of the PCR products within the gene region encoding the cell wall-spanning domain indicated a high degree of genetic variability. Thirteen different variants of the amplified region were differentiated among the 60 Cbeta-protein-positive isolates by sequence analysis. In all variants, the polymorphisms were caused by insertions and deletions of repetitive DNA elements that did not alter the open reading frame. Comparison of the Cbeta-protein gene polymorphisms showed a significantly higher rate of isolates carrying deletions >50 bp in serotype Ib than in serotype II isolates (p = 0.001); this was also true for neonatal isolates analyzed separately (p = 0.01). Neonatal isolates carried a higher rate of large deletions when compared with maternal isolates; this difference, however, did not reach statistical significance (p = 0.08). We hypothesize that polymorphisms in the cell wall-spanning domain of the Cbeta-protein are of functional relevance with regard to maternofetal transmission of the pathogen.