The annual incidence of meningococcal disease (meningitis and septicaemia) in Taiwan was 0·94/105 population in 1953. It then declined to below 0·001 from 1980 to 1987, and re-emerged in 2000 with a rate of 0·07/105 population. In 2001 there was a further increase in incidence (43 cases, 0·19/105). Of 43 isolates of Neisseria meningitidis available for this study, including 41 from patients treated in 2001, three (7·0%) were penicillin insensitive (MIC [ges ]0·12 μg/ml), though all were β-lactamase negative; 16 (37·2%) were resistant to trimethoprim–sulphamethoxazole sulphamethoxazole (MIC [ges ]4/76 μg/ml). Serogrouping and genotype analysis revealed nine domestic clones. None of the 43 patients had any relationship (travel or contact history) with the 2000 or 2001 Hajj pilgrimage. Epidemiological information and typing results suggested wide dissemination of a limited number of domestic clones of N. meningitidis, manifesting as serogroups W-135, B and Y. Two clones of serogroup W-135 involved in the outbreak were genetically distinct from the 2000 or 2001 Hajj-related W-135 clone.