Unequal arterial stiffness had been associated with cardiovascular risks. We investigated whether an association existed between unequal arterial stiffness indicated by bilateral brachial-ankle pulse wave velocity (baPWV) difference and ankle-brachial index (ABI), baPWV, echocardiographic parameters and interarm and interankle systolic blood pressure (BP) differences. A total of 1111 patients referred for echocardiographic examination were included in this study. The BPs, ABI and baPWV were measured simultaneously by an ABI-form device. The ΔbaPWV was defined as absolute value of difference between bilateral baPWV. We performed three multivariate analyses for determining the factors associated with a ΔbaPWV ≧ 185 cm/s (90 percentile of ΔbaPWV) (model 1: significant variables in univariate analysis and ABI <0.9 and baPWV; model 2: significant variables in univariate analysis and left ventricular mass index [LVMI]; model 3: significant variables in univariate analysis and interankle systolic BP difference ≧ 15 mmHg). The ABI <0.9 and high baPWV (both P<0.001) in model 1, high LVMI (P = 0.021) in model 2 and an interankle systolic BP difference ≧ 15 mmHg (P = 0.026) in model 3 were associated with a ΔbaPWV ≧ 185 cm/s, but the interarm systolic BP difference ≧ 10 mmHg was not (P = NS). Our study demonstrated ABI <0.9, high baPWV, high LVMI and an interankle systolic BP difference ≧ 15 mmHg were associated with unequal arterial stiffness.