Abnormalities of proteoglycan, collagen, and elastic fibers were found in floppy mitral valves. Perlecan is one of the three major classes of heparan sulfate proteoglycans within the cardiovascular system. The role of perlecan genetic variant in mitral valve prolapse (MVP) has not been studied. We therefore performed a case-controlled study investigating the possible relation between the perlecan gene intron 6 BamHI polymorphism and MVP among the Chinese population in Taiwan. We studied 100 patients with MVP diagnosed by echocardiography and 100 age- and sex-matched normal control subjects. The perlecan gene intron 6 BamHI polymorphism was identified by polymerase chain reaction-based restriction analysis. There were no significant differences in either the genotype distribution or allelic frequencies between MVP cases and controls for perlecan gene intron 6 BamHI polymorphism (P = 0.20 and 0.76, respectively). Further categorization of the MVP patients into mild and severe subgroups also revealed no statistical difference from controls for perlecan gene intron 6 BamHI polymorphism. It is concluded that perlecan gene intron 6 BamHI polymorphism is not a suitable genetic marker of MVP in Taiwan Chinese.