The meningococcal capsule is the primary virulence factor with systemic isolates requiring full expression of the capsule but with capability to down-regulate the capsule in order to invade. The meningococcal capsular operon is composed of a number of genes that are involved in capsular synthesis and transport. Differences in capsular synthesis genes may allow discrimination between meningococcal serogroups whereas absence of genes for either synthesis or transport imply that the meningococcus is unencapsulated. Although mechanisms such as slipped-strand mispairing and acquisition of insertion sequences have been demonstrated to be involved in regulation of capsular expression, few studies have addressed the mechanisms of capsular expression in carrier isolates. Following a community-based intervention programme for an outbreak of meningococcal disease, we collected meningococcal carrier isolates from the intervention area and control areas. We undertook genetic analysis of the capsular operon and the mechanisms of capsular regulation, together with an investigation of the potential of capsular genes to identify the genogroup of non-serogroupable isolates. Use of the siaD gene allowed the discrimination of 30/89 (34%) non-serogroupable isolates into B, C, W135 and Y with a siaA gene PCR permitting the characterization of a further 6 isolates whose capsules contained sialic acid. Slipped-strand mispairing was evident in only 4 of 13 genogroupable B isolates and the insertion sequence IS1301 was found in 2 of 36 siaA-positive isolates. Of 51 non-genogroupable isolates 25 (49%) were shown to be ctrA negative. There was a higher percentage of ctrA-positive isolates (P<0·001) amongst meningococcal strains obtained from those sampled in non-intervention schools than those sampled at intervention schools. The ctrA-negative isolates warrant further investigation of their genotypic organization since such avirulent strains may be important in conferring natural protection against invasive disease. We found that after mass antibiotic prophylaxis, recolonization occurs preferentially with non-pathogenic meningococcal strains. This has implications for assessment of the benefits of mass antibiotic and vaccination programmes for outbreak control. Previously expressed concerns of increased risk due to removal of protective flora may have been overstated.