The human gelatinase B (MMP-9) gene promoter region contains a CA microsatellite repeat and a single nucleotide polymorphism which are known to influence transcriptional activity. These two polymorphisms were used to investigate the existence of an association between multiple sclerosis (MS) susceptibility and the MMP-9 gene. In a case-control analysis of 345 Swedish individuals and in a study of 125 Sardinian simplex families no genetic associations between the gelatinase B gene polymorphisms and MS susceptibility were found. These data reinforce the suggestion of epistasis in the regulation of the metalloproteinase-inhibitor balance in MS.