We analysed cerebrospinal fluid samples from suspected meningitis cases in Nouna Health District, Burkina Faso, during the meningitis seasons of 2004-2006. Serogroup A ST2859 meningococci belonging to the ST5 clonal complex of subgroup III meningococci were the predominant causative agent. ST2859 bacteria were associated with focal outbreaks in the north of the district. While >10% of the population of an outbreak village carried ST2859, the population in the south of the district was predominantly colonised by serogroup Y ST4375 meningococci, which were associated with only sporadic cases of meningitis. Colonisation with the less virulent Y meningococci may interfere with the spread of the ST2859 to the south of the district, but there are concerns that this serogroup A clone may cause a third wave of subgroup III meningococcal disease in the African Meningitis Belt.