Competence for genetic transformation in Streptococcus pneumoniae is regulated by a quorum-sensing mechanism involving the pheromone competence stimulating peptide (CSP) encoded by comC and a two-component signal transduction system, ComD-ComE (TCS12). In the presence of CSP, the transmembrane histidine kinase ComD receptor activates the response regulator ComE. The comC, comD and comE genes are part of an operon denoted as comCDE. In this work, the comCDE locus of 17 S. pneumoniae strains was characterized by DNA sequencing. Two major allelic combinations, comC1-comD1 and comC2-comD2 were present. Two further allelic combinations, comC1-comD3 and comC1-comD4, were also present. Comparison of the deduced amino acid sequences of the four ComD allelic variants showed that all variations are localized in the N-terminal sensor domain. In order to have the four comD alleles in the same genetic background, we constructed four different isogenic strains in which comC was deleted and the DNA encoding the sensor domain of ComD was exchanged. To formally demonstrate that the sensor domain of ComD is responsible for competence pherotype specificity, CSP-1 and CSP-2 peptides were used to induce competence in the isogenic strains: (i) strains expressing the ComD1, ComD3 and ComD4 variants were induced to competence by CSP1; (ii) the strain expressing ComD2 was induced by CSP2. Moreover, cross-induction of competence by both CSPs was observed in the ComD2 and ComD3-carrying strains in the presence of high CSP doses. This is the first formal confirmation that the ComD sensor domain is responsible for competence pherotype specificity in S. pneumoniae.