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Neisseria meningitidis W-135 accounted for nine (1.6%) of 562 cases of invasive meningococcal disease and 17 (3.9%) of 430 meningococcal isolates from healthy carriers. There was no mortality associated with the invasive nine isolates, which belonged to subtype P1.6 and geno-subtype P1.18–1. All invasive isolates and 15 of the 17 isolates from healthy carriers belonged to sequence type 22 by multilocus sequence typing, and showed a similarity of > 85% by pulsed-field gel electrophoresis following digestion with Nhe I. These results demonstrate that W-135 isolates in the Basque region of northern Spain have a high degree of similarity and are almost clonal.