We analyzed 48 invasive isolates of Neisseria meningitidis that were isolated from meningitis cases in Burkina Faso (April 2002 to April 2003). Thirty-nine of these isolates had the phenotype (serogroup:serotype:serosubtype) W135:2a:P1.5,2, eight isolates were A:4:P1.9 and one isolate was nongroupable:nonserotypable:nonserosubtypable. Genotyping of meningococcal isolates showed that W135 isolates belonged to the sequence type (ST)-11. The nongroupable isolate was of genogroup W135 and belonged to ST-192. Isolates of serogroup A belonged to ST-2859 (a member of the subgroup III/ST-5 clonal complex). W135 (ST-11) isolates involved in meningitis outbreaks in Burkina Faso differed from those involved in the Hajj-2000 associated outbreak by their pulsed-field gel electrophoresis profile. These data confirm the changing epidemiology of meningococcal infection in Burkina Faso with the establishment and expansion of serogroup W135 N. meningitidis strains of the ET-37/ST-11 clonal complex, as well as the emergence of a new clone within the subgroup III/ST-5 clonal complex.