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To assess whether there is a natural difference in blood pressure (BP) measurements between the right and left arms, and to identify what factors are associated with this difference in a general population.The study subjects were 1090 individuals who participated in a medical check-up in Ohasama, Japan. The BP was measured simultaneously in both arms, using an automated device. The inter-arm BP difference was expressed as the relative difference [right-arm BP (R) minus left-arm BP (L): R – L] and the absolute difference (|R – L|). The relationship between inter-arm difference and various factors was analyzed using univariate analysis. The characteristics of subjects in whom the absolute systolic BP (SBP) difference was greater than 10 mmHg were analyzed using multivariate logistic analysis.The relative differences in SBP and diastolic BP (DBP) were −0.6 ± 6.6 (mean ± SD) and 1.1 ± 4.7 mmHg, while the absolute differences were 4.9 ± 4.4 and 3.7 ± 3.0 mmHg. The absolute SBP difference was found to correlate significantly with age, body mass index, ankle–brachial index (ABI), and hypertension. Subjects with hypertension, hypercholesterolemia, obesity, elevated hemoglobin A1c (HbA1c) and low ABI had a significant and independent increase in the risk of an absolute SBP difference greater than 10 mmHg.The results suggest that there is considerable difference in the measured BP in the right and left arms and that large differences in the absolute SBP are associated with risk factors for arteriosclerosis such as hypertension, hypercholesterolemia, obesity, metabolic abnormalities and low ABI.