Objective To investigate the significance of matrix metalloproteinase-9 (MMP-9) and tissue inhibitor of metalloproteinase-1 (TIMP-1) in serum and cerebrospinal fluid for evaluation of severe hand, foot, and mouth disease (HFMD) complicated with neurogenic pulmonary edema (NPE). Methods A total of 140 patients diagnosed with HFMD in Henan Children′s Hospital were enrolled and divided into three groups including mild group, severe HFMD group without NPE , severe HFMD group with NPE .These severe HFMD patients were also divided into survival group and death group according to the 28-day prognosis. Meanwhile, 50 age-matched healthy children were selected as controls. Serum MMP-9 and TIMP-1 levels were measured in all enrolled children. At the same time, MMP-9, TIMP-1 and ratio of MMP-9/TIMP-1 in cerebrospinal fluid were measured in the severe HFMD group with and without NPE. Quantitative data were compared using one-way analysis of variance, and means comparisons between samples were conducted using LSD- t test. Results Among 140 children with HFMD, 66 were in mild group, 42 in severe HFMD without NPE group, and 32 in severe HFMD with NPE group. And 50 healthy children were in control group. After 28 days, 14 cases died in severe HFMD groups. MMP-9, TIMP-1 and MMP-9/TIMP-1 in serum of severe HFMD group with NPE increased significantly greater than those in the other three groups (F=269.356, 121.301 and 101.502, respectively, all P <0.05). MMP-9, TIMP-1 and MMP-9/TIMP-1 in cerebrospinal fluid of severe HFMD group with NPE were (57.24±8.92) μg/L, (35.26±8.14) μg/L and (1.66±0.23) μg/L, respectively, while those in cerebrospinal fluid of severe HFMD group without NPE were (30.57±3.89) μg/L, (26.25±0.32) μg/L and (1.17±0.61) μg/L, respectively. The differences between the two groups were all statistically significant (t=62.485, 37.680 and 169.387, respectively, all P<0.01). MMP-9, TIMP-1 and MMP-9/TIMP-1 in serum and cerebrospinal fluid of death group increased significantly greater than those in survival group, the difference were statistically significant (all P<0.01). The maximum area under curve (AUC) was reached when the MMP9/TIMP-1 ratio in cerebrospinal fluid was 0.890 (95% CI: 0.801-0.978). Conclusions MMP-9 and TIMP-1 may be involved in the pathogenesis of HFMD complicated with NPE. The detection of MMP-9 and TIMP-1 levels may be beneficial for the early diagnosis of severe HFMD with NPE. The imbalance of MMP-9/TIMP-1 ratio can be used as one of the predictors of severe HFMD combined with NPE. Key words: Matrix metalloproteinase 9; Hand, foot and mouth disease; Pulmonary edema; TIMP-1