Allelic association methods are better suited than linkage analysis for mapping of susceptibility genes that confer modest increases in risk in complex diseases. In both family- and population-based association studies, it is very useful to have prior knowledge of all sequence variants and the degree of linkage disequilibrium in a candidate gene region. In this study, we scanned sequence variants in a 2.2-kb promoter sequence and all 13 exons (totalling 3.3 kb) of the matrix metalloproteinase-9 gene, which is associated with coronary heart disease and a candidate for other diseases involving connective tissue remodelling, such as cancer metastasis. The sequences had a total of ten variable sites, four in the promoter, five in the coding region (three of which alter the amino acid encoded) and one in the 3' untranslated sequence. Sequence inspection suggests that some of the variants will have a functional impact on either level of expression or enzymatic activity. Tight linkage disequilibrium was detected between variants across the entire length of the gene (approximately 9 kb), and frequencies of different haplotypes were determined. The data provide an essential tool for studies of the possible contribution of genetic variation at the matrix metalloproteinase-9 locus to genetically determined susceptibility to a number of important diseases. The results also provide experimental data on the extent of linkage disequilibrium in the general population, which is yet to be resolved.