A total of 87 invasive isolates of Haemophilus influenzae isolated throughout Taiwan from 1994 to 1998 was collected; 57 were from children <14 years old. In all, 60.9% of isolates were resistant to ampicillin and produced beta-lactamase. Ribotyping revealed six different profiles in 55 isolates of type b, nine profiles in 10 isolates of non-type b and 12 profiles in 22 isolates of non-typable H. influenzae. Among isolates from 35 cases of meningitis, 30 (86%) were in ribogroups 1, 2 and 3 with >90% genetic similarity. Compared with all the other ribogroups, ribogroups 1, 2 and 3, which encompassed all H. influenzae type b, were significantly more prevalent as a cause of meningitis in children <14 years old. Further subtyping of the predominant ribogroup by pulsed-field gel electrophoresis (PFGE) identified differences of 0-6 bands among these isolates of ribogroup 1, which indicated distant relatedness. Automated ribotyping was found to be a useful method and was less time-consuming for molecular epidemiology studies of H. influenzae. PFGE is suggested as an addition to ribotyping to improve discrimination if H. influenzae type b is involved. Differentiating ribogroups between type b and non-type b H. influenzae by genotyping may help to understand the molecular characteristics of outbreaks, endemicity and value of vaccination. According to the results of ribotyping and PFGE, it seems possible that spread of invasive H. influenzae type b had occurred and ribotyping confirmed that there was no clonal spread of non-type b H. influenzae in Taiwan.