The pathogenesis of non-herpetic acute limbic encephalitis (NHALE) has been not clear. Matrix metalloproteinase-9 (MMP-9) and tissue inhibitor of metalloproteinase 1 (TIMP-1) play important roles in the function of the blood-brain barrier. We measured the serum concentrations of MMP-9 and TIMP-1 by using enzyme-linked immunosorbent assay (ELISA) in 23 patients with NHALE in the acute and convalescent stages. Serum MMP-9 concentrations and ratios of serum MMP-9/TIMP-1 were significantly higher (1) in patients with NHALE in acute and convalescent stages than in control patients (all P < 0.001); (2) in patients with NHALE at the acute stage compared with those at the convalescent stage (P = 0.004, and P = 0.014, respectively). In contrast, serum TIMP-1 concentrations were significantly lower in patients with NHALE in the acute and convalescent stages than in control patients (both P < 0.001) but did not differ in patients with NHALE in the acute and convalescent stages. Our preliminary study suggests that the prolonged imbalance of MMP-9 and TIMP-1 is associated with the pathogenesis of NHALE.