First results of multilocus sequence typing (MLST) of Haemophilus influenzae strains are presented. MLST of 28 H. influenzae strains isolated from patients with invasive diseases in the Czech Republic is indicative of clonal homogeneity of these strains: 22 out of 26 H. influenzae b strains tested were of the same sequence type, ST-6. Four strains were of two sequence types newly described in this study: ST-83 (3 strains) and ST-84 (1 strain). Two nontypeable H. influenzae strains were assigned to sequence types other than ST-6: ST-3 and ST-85 newly described in this study. First MLST results show ST-6 to be typical of H. influenzae b isolated from patients with invasive diseases in the Czech Republic. The sequence types newly described in this study, i.e. ST-83, ST-84 and ST-85, were submitted to the worldwide H. influenzae MLST database (http://haemophilus.mlst.net).