BACKGROUND: The morning heart rate surge (MHRS) and morning blood pressure surge (MBPS) may be responsible for the high prevalence of cardiovascular events during the morning period. The clinical significance of the MBPS has been well established, but that of the MHRS remains unclear. Thus, we evaluated the association between the MHRS and target organ damage (TOD). METHODS: A cross-sectional study of 580 hypertensive patients was performed. MHRS and heart rate variability (HRV) were analyzed by 24 h electrocardiogram. TOD was assessed by estimated glomerular filtration rate, carotid intima-media thickness (IMT), and left ventricular mass index. RESULTS: The prevalence of TOD tended to decrease with sleep-trough MHRS (first to fourth quartiles: 71%, 70.3%, 58.6%, and 52.7%, respectively) or prewaking MHRS quartiles (first to fourth quartiles: 65.3%, 73.6%, 61.4%, and 54.2%, respectively), whereas the opposite trend was observed for standard deviation of all normal NN intervals (SDNN). Moreover, sleep-trough MHRS, prewaking MHRS, SDNN, and SDNN index were significantly lower in patients with TOD than in those without TOD. According to four logistic regression models, the associations of prewaking MHRS, SDNN, and SDNN index with TOD were lost after adjustment for age and BP. Patients in the first (</=11.125 bpm) and second sleep-trough MHRS quartiles (11.125-15.75 bpm) had a 1.95-2.06-fold increased risk of TOD compared with those in the fourth quartile (p < 0.05). CONCLUSION: A blunted sleep-trough MHRS, which may serve as a surrogate marker for autonomic imbalance, was independently associated with TOD in primary hypertensive patients.