Both blood pressure (BP) non-dipping and nighttime hypertension have been associated with accelerated target-organ damage (TOD). However, increased nighttime BP in subjects with a dipping circadian BP profile has never been reported or associated with TOD. Here, we investigated the relationships of nighttime BP with indices of vascular and kidney damage in dipper hypertensive subjects. We studied 402 subjects with untreated stage I-II essential hypertension. According to ambulatory BP recordings, 127 dipper subjects were selected and subdivided into nighttime hypertensives (NH, n = 69) (nighttime BP ≥ 120/70) and nighttime normotensives (NN, n = 50) (nighttime BP <120/70 mm Hg). All participants underwent echocardiographic examination and assessments of carotid-to-femoral pulse wave velocity (c-f PWV), albumin-to-creatinine ratio (ACR), metabolic profile and high sensitivity C-reactive protein (hs-CRP) level. Compared with NN dippers, NH dippers had higher c-f PWV (P < 0.001), ACR values (P = 0.01) and hs-CRP levels (P < 0.001). Multiple regression analysis showed that nighttime BP was more correlated with c-f PWV and ACR than was daytime BP. Among dippers, nighttime BP is associated more closely with c-f PWV and ACR than is daytime BP. These findings imply that even in dippers, absolute nighttime BP values should be taken into account when predicting surrogate end points such as arterial stiffness and urinary albumin excretion.