Elevated levels of matrix metalloproteinase-9 (MMP-9) associates with predictors of multiple sclerosis (MS) activity. We analysed serum levels and mRNA expression of MMP-9 and its inhibitor TIMP-1 in peripheral mononuclear cells of 14 MS patients after autologous hematopoietic stem cell transplantation (AHSCT). All but 2 patients stabilized after AHSCT. A significant decrease of MMP-9 levels was seen up to 36 months after AHSCT. TIMP-1 levels did not change. MMP-9 mRNA levels correlated with the CD4+ T cell count (p<0.0001). The significant and persistent change in MMP-9 activity after AHSCT may be caused in part by the effect of AHSCT in the CD4+ T cell count.