In the past decades efforts to further diminish the case-fatality rate from meningococcal disease have proven challenging due to the often rapid progression of the disease in patients. In this study our objective was to characterise a subset of Neisseria meningitidis isolates to establish which sequence types were associated with increased mortality in Denmark during the period 2000-2007. We designed a matched case control and performed serogrouping, serotyping, serosubtyping and multilocus sequence typing (MLST) on 100 isolates. The clonal complex ST-32/ET-5 was found in 36% of the isolates, followed by the ST-11/ET-37 complex (14%) and ST-41/44 complex/Lineage 3 (14%). Eight new sequence types were found. None of the clonal complexes were significantly associated with increased mortality. Phenotype B:15:P1.7,16 tended to be a better predictor of death than ST-32. Although the numbers were low, the present study indicates that phenotyping may be a better predictor of mortality than MLST, which suggests that each typing method has its advantages and disadvantages. If this notion can be confirmed by other studies, it may stimulate additional research regarding the pathogenesis of severe illness, for example, if certain surface molecules trigger a cytokine storm more than others.