Hepatitis B virus (HBV) and hepatitis C virus (HCV) are the two major causes of chronic liver inflammation, fibrosis and cirrhosis. They have the ability to cause persistent infection in susceptible hosts and severely damage liver function. Matrix metalloproteinase-9 (MMP-9) is one of the gelatinases that may be important in liver fibrosis. This study aims to evaluate whether or not MMP-9 in relation to viral load is involved in the development of liver dysfunction in HBV and HCV Blood samples from 20 patients chronically infected with HBV and 30 with HCV, along with 15 healthy individuals as controls, were investigated. Viral load was assessed by real-time polymerase chain reaction (PCR). Serum MMP-9 levels were evaluated by enzyme-linked immunosorbent assay (ELISA). Alanine transaminase and aspartate aminotransferase (ALT and AST) activities were measured spectrophotometrically. Levels of MMP-9 were significantly higher in HCV than in HBV patients (P < 0.01), and positively correlated with HBV viral load (r = 0.842, P < 0.01) and AST:ALT ratio (r = 0.614, P < 0.05). Conversely, MMP-9 levels did not correlate with HCV viral load but did correlate with AST:ALT ratio (r = 0.652, P < 0.01). Therefore, MMP-9 levels could reflect progressive liver damage in HBV and HCV infection. However, a distinction between the pathological mechanism of HCV and HBV is suggested, as HCV probably promotes hepatocyte damage and fibrosis through mechanisms other than replication. Continuous expression of the HBV genome through replication and secretion of viral antigens may contribute to the transcriptional regulation of MMP-9, thus promoting liver damage and fibrosis.