Although oral melatonin administration may enhance a nocturnal blood pressure fall, it remains unclear whether endogenous melatonin, which is present at considerably lower levels than pharmacological melatonin, is associated with the non-dipper pattern. The present cross-sectional study aimed to determine the association between urinary melatonin excretion, an index of endogenous melatonin, and the non-dipper pattern. We measured the following variables in 141 elderly hypertensives: overnight urinary melatonin excretion, ambulatory blood pressure and actigraphic physical activity. We defined a non-dipper pattern as a <10% fall in sleep systolic blood pressure compared with awake systolic blood pressure. When participants were divided into two groups (high and low melatonin groups) by the cutoff value for identifying the top tertile, the characteristics, except for age, did not significantly differ between the two groups. Crude logistic regression analysis showed significant associations of the non-dipper pattern with age, diabetes, higher urinary melatonin excretion (high vs. low) and daytime activity. In a multivariate analysis after adjustment for age, diabetes and daytime activity, the odds ratio for the non-dipper pattern in the high melatonin group was significantly lower than that in the low melatonin group (odds ratio: 0.39, 95% confidence interval (CI): 0.17-0.91, P=0.03). Moreover, the mean percentage systolic blood pressure nocturnal fall, adjusted for the former covariates, was significantly higher in the high melatonin group than the low melatonin group (difference 3.5%, 95% CI: 0.0-7.0%, P=0.048). Among elderly hypertensive individuals, nocturnal urinary melatonin excretion is significantly and inversely associated with the non-dipper pattern.