Severe malaria, including cerebral malaria (CM), is characterized by the sequestration of parasitized erythrocytes in the microvessels after cytoadherence to endothelial cells. Products of parasite origin, such as haemozoin (HZ), contribute to the pathogenesis of severe malaria by interfering with host inflammatory response. In human monocytes, HZ enhanced the levels of matrix metalloproteinase-9 (MMP-9), a protease involved in neuroinflammation. Here the effects of HZ on the regulation of MMPs by the human microvascular endothelial cell line HMEC-1 were investigated. Cells treated with natural (n)HZ appeared elongated instead of polygonal, and formed microtubule-like vessels on synthetic basement membrane. nHZ enhanced total gelatinolytic activity by inducing proMMP-9 and MMP-9 without affecting basal MMP-2. The level of the endogenous tissue inhibitor of MMP-9 (TIMP-1) was not altered by nHZ, while TIMP-2, the MMP-2 inhibitor, was enhanced. Additionally, nHZ induced MMP-1 and MMP-3, two enzymes sequentially involved in collagenolysis and proMMP-9 proteolytic activation. Lipid-free HZ did not reproduce nHZ effects. Present data suggest that the lipid moiety of HZ alters the MMP/TIMP balances and promotes the proteolytic activation of proMMP-9 in HMEC-1, thereby enhancing total gelatinolytic activity, cell activation and inflammation. These findings might help understanding the mechanisms of blood brain barrier damage during CM.