Matrix metalloproteinases (MMPs) and their tissue inhibitors (TIMPs) play an important role in cardiovascular remodeling. The aim of the study was to analyze MMP/TIMP genes expression in peripheral blood leukocytes of 80 hypertensive children (15.1 ± 2.0 years) in comparison with age-matched 78 normotensive children (14.6 ± 2.0 years; n.s.). TIMP and MMP expression in peripheral blood leukocytes was assessed by quantitative real-time PCR. Hypertensive children independently of age, sex, and body mass index had greater expression of MMP-2 than normotensive controls (p = 0.0001). Patients with left ventricular hypertrophy had greater expression of MMP-14 than patients with normal left ventricular mass (p = 0.006) and TIMP-2 expression correlated with carotid wall cross-sectional area (p = 0.03; r = 0.238). MMP-14 expression correlated with BMI-SDS (p = 0.001; r = 0.371), waist circumference-SDS (p = 0.016; r = 0.290), hsCRP (p = 0.003; r = 0.350), serum HDL-cholesterol (p = 0.008; r = -0.304), and serum uric acid (p = 0.0001; r = 0.394). In conclusion, hypertensive adolescents presented significant alterations of MMP/TIMP expression pattern in comparison with normotensive peers. Moreover, altered MMP/TIMP expression was associated with hypertensive target organ damage and metabolic abnormalities.