Extracellular matrix proteins (ECM) are important for migration and correct positioning of postmitotic neurons. They also contribute to the proper patterning of synaptic connectivity and modulate the structure and functions of synaptic circuitry. Matrix metalloproteinases (MMPs) can degrade a range of extracellular matrix proteins. MMP-3 (also called Stromelysin 1) is an important member of MMP family. In this study, we aimed to investigate whether MMP3 polymorphic variants are involved in bipolar affective disorder, their relatives and normal subjects. There was not difference in the age between patients and controls. MMP-3 5A/6A polymorphism was determined by restriction fragment length polymorphism. The genotype distributions for MMP3 5A6A were 14.9% 5A5A, 46.3% 6A6A, 38.8% 5A6A in patients; 15.1 % 5A5A, 46.2 % 6A6A, 38.7 % 5A6A in relatives and 12 % 5A5A, 53 % 6A6A, 35 % 5A6A in controls. The distributions of MMP3 genotypes were not statistically different among all groups. Our results have suggested that there were no association between MMP3 polymorphism and bipolar affective disorder.