Circadian blood pressure variability and melatonin secretion are both regulated by the biological clock. Several clinical trials have suggested that oral administration of exogenous melatonin lowers blood pressure at night, although it remains unclear whether melatonin secretion, which is considerably lower than pharmacological melatonin levels, is associated with nighttime blood pressure. In this cross-sectional study, we measured overnight urinary melatonin excretion, which is an index of melatonin secreted, along with ambulatory blood pressure. Of 863 participants (mean age, 72.1 years), 386 participants received some form of antihypertensive drug treatment. With a quartile increase in urinary melatonin excretion, nighttime systolic blood pressure significantly decreased in the untreated group (P-value for trend=0.01), whereas neither association was observed in the treated group (P-value for trend=0.87). Among the untreated group, multivariate linear regression models revealed that higher log-transformed urinary melatonin excretion was significantly associated with decreased nighttime systolic blood pressure, independently of age, gender, body mass index, current smoking status, diabetes, daytime physical activity, duration in bed (scotoperiod) and day length (photoperiod) (regression coefficient: -2.21; 95% confidence interval: -4.38 to -0.05, P=0.045). This association suggests that an increase in the urinary melatonin excretion from 4.2 to 10.5 μg (25th to 75th percentile) is associated with a 2.0 mm Hg decrease in nighttime systolic blood pressure. In conclusion, melatonin secretion is significantly and inversely associated with nighttime blood pressure in a general elderly population without antihypertensive drug treatment. This association was not observed in treated elderly individuals.