A positive association of MAOA polymorphisms with alcoholism has been demonstrated in certain recent studies, however, this association is not universally supported. The haplotype status of the MAOA gene polymorphisms could provide more information than alleles at a single site alone tested for an association with a complex, heterogeous disorder. This study examines whether there is an association between alcoholism and either a variable number of tandem repeat located upstream of the MAOA gene or an EcoRV functional polymorphism of the MAOA gene. These are analyzed both individually and as haplotypes. The study consisted of 214 subjects meeting DSM-IV criteria for alcoholism from northern Taiwan and 77 control individuals without history of alcoholism from Taipei. All of the subjects were Chinese Han males. For the two polymorphic sites, significant linkage disequilibrium occurred. No significant intergroup difference was observed between the two subject groups with respect to the allele frequencies for the two polymorphisms at the MAO locus tested both individually and as haplotypes. This finding suggests that no association exists between genetic variation at the MAOA locus and alcoholism in Chinese Han males.