Background: Central aortic pressure has often been shown to be more closely associated with markers of vascular function and incidence of cardiovascular events compared to peripheral pressure. However, the potential clinical use of central aortic or peripheral haemodynamic indices as markers of target organ damage (TOD) has not been fully established. Methods: We evaluated associations of TOD with central aortic and peripheral haemodynamic indices (central aortic [cPP] and peripheral pulse pressure [pPP], central aortic augmentation index, and central and peripheral waveform factor) in 770 hospital inpatients (age 60 ± 10 years, 473 males) with primary hypertension. TOD was quantified in terms of arterial stiffness as measured by carotid-femoral pulse wave velocity (cfPWV), carotid intima-media thickness (IMT), and urine albumin-to-creatinine ratio (ACR). Subclinical TOD was defined as carotid IMT >0.9 mm, urine ACR >3.5 mg/mmol in females and >2.5 mg/mmol in males and/or cfPWV >12 m/s. Results: Both cPP and pPP showed significant correlation with cfPWV (r = 0.41 vs. 0.40; p < 0.01), ACR (r = 0.24 vs. 0.27; p < 0.01) and carotid IMT (r = 0.14 vs. 0.15; p < 0.01). Each SD increase in pPP and cPP was associated with increased risk of cfPWV >12 m/s (odds ratio [OR] = 2.7 and 2.9 for pPP and cPP, respectively), ACR >2.5 mg/mmol (OR = 1.2 and 1.4, respectively), and carotid IMT >0.9 mm (OR = 1.46 and 1.53, respectively). Compared to pPP, cPP had higher predictive power for TOD for age ≥60 years (OR = 3.07, p < 0.001). Conclusions: Although both pPP and cPP show an association with TOD in a hypertensive population, cPP provides additional information beyond pPP associated with TOD in a hypertensive cohort. Central aortic haemodynamic indices as potential biomarkers of subclinical TOD need to be validated by further prospective studies.