Background Cathepsin Sand its endogenous inhibitor cystatin Care implicated in the pathogenesis of atherosclerosis, especially in the plaque destabilization and rupture leading to acute coronary syndrome. However, whether circulating cathepsin S and cystatin C also change in association with coronary plaque morphology is unknown yet. Methods We recruited 98 patients with unstable angina (UA, n=56) or stable angina (SA, n=42) who had a segmental stenosis resulting in >20% and <70% diameter reduction in one major coronary artery on coronary angiography. Thirty-one healthy subjects served as controls. Intravascular ultrasound (IVUS) was used to evaluate plaque morphology. Plasma cathepsin S and cystatin C were measured as well. Results At the culprit lesion site, plaque area ((7.85 +/- 2.83) mm(2) vs (6.53 +/- 2.92) mm(2), P=0.027), plaque burden ((60.92 +/- 11.04)% vs (53.87 +/- 17.52)%, P=0.025), remodeling index (0.93 +/- 0.16 vs 0.86 +/- 0.10, P=0.004) and eccentricity index (0.74 +/- 0.17 vs 0.66 +/- 0.21, P=0.038) were bigger in UA group than in SA group. Plasma cathepsin S and cystatin C were significantly higher in patients than in controls (P <0.01). Plasma cathepsin S was higher in UA group ((0.411 +/- 0.121) nmol/L) than in SA group ((0.355 +/- 0.099) nmol/L, P=0.007), so did the plasma cystatin C ((0.95 +/- 0.23) mg/L in UA group, (0.84 +/- 0.22) mg/L in SA group; P=0.009). Plasma cathepsin S positively correlated with remodeling index (r=0.402, P=0.002) and eccentricity index (r=0.441, P=0.001), and plasma cystatin C positively correlated with plaque area (r=0.467, P <0.001) and plaque burden (r=0.395, P=0.003) in UA group but not in SA group. Conclusions Plasma cathepsin S and cystatin C increased significantly in UA patients. In angina patients, higher plasma cathepsin S may suggest the presence of vulnerable plaque, and higher plasma cystatin C may be a clue for larger atherosclerotic coronary plaque. Chin Med J 2009;122(23):2820-2826