Background: Identification of subclinical target organ damage (TOD) at early stage is important for the reduction in cardiovascular risk. This study was performed to assess the association between metabolic syndrome (MetS) and several types of TOD in urban people. Methods: Data from 958 Korean subjects without cardiovascular disease, living in Seoul city (mean age, 55.2 years, 47.6% males), were extracted from the prospective cohort database. All participants underwent extensive evaluation of TOD parameters, including left ventricular mass index (LVMI), E/e', brachial-ankle pulse wave velocity (baPWV), estimated glomerular filtration rate (eGFR), ankle-brachial index (ABI), carotid intima-media thickness (IMT), and obstructive coronary artery disease. Results: MetS and ≥1 TOD were detected in 494 (51.5%) and 329 (34.3%) subjects, respectively. There were no significant differences in the prevalence of ≥1 TOD according to the presence of MetS (P > 0.05). Among MetS components, only high blood pressure was associated with ≥1 TOD (69.6% vs. 59.9%, P = 0.004). There was a positive association between ≥1 TOD and the number of MetS traits (P = 0.034). There were significant linear correlations of Z-score of MetS with baPWV (r = 0.241, P < 0.001) and eGFR (r = -0.173, P < 0.001) but not with LVMI, E/e', ABI, and carotid IMT (P > 0.05 for each). Conclusions: In urban Korean population without cardiovascular disease, TOD is more closely related to the number of risk factors meeting MetS criteria and high blood pressure than the presence of MetS itself.