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Objectives: Chronic kidney disease (CKD) is a well-established risk factor for cardiovascular diseases. Studies in adults have demonstrated the association between mildly decreased kidney function or even normal values of markers of kidney function to pulse wave velocity (PWV), a measure of arterial stiffness and a predictor of cardiovascular events. Our study aimed to evaluate associations between markers of CKD, PWV, and central haemodynamic parameters in children and adolescents at risk of subclinical kidney damage. Methods: 182 children and adolescents with hypertension, obesity, or hypercholesterolaemia (risk factors for subclinical kidney damage) were included in the study. The subjects were subdivided into 4 groups comprising children and adolescents with hypertension (group 1), obesity (group 2), hypercholesterolaemia (group 3), and a group with a combination of risk factors, such as obesity-related hypertension and metabolic syndrome (group 4). The study groups were compared to a group of healthy controls (group 5). PWV was measured by applanation tonometry (SphygmoCor, SCOR-Vx, Sydney, NSW, Australia) and laboratory parameters (serum creatinine, serum cystatin C, and microalbuminuria) were collected. Results: Pearson’s correlation coefficient demonstrated a statistically significant correlation between PWV and serum creatinine in group of all subjects (r = 0.220, p = 0.002). Further subdivision showed the correlation was significant in group 4 (r = 0.370, p = 0.002). In group 2 a correlation between PWV and cystatin C was found (r = −0.535, p = 0.009). In multiple regression analysis of all subjects with PWV as the dependent variable, age and diastolic blood pressure were statistically significant. Correlations between markers of kidney function and central haemodynamic parameters also showed significant correlations between serum creatinine and heart rate (HR) (r = −0.476, p < 0.001) as well as associated parameters (augmentation index, standardized at HR 75/min, ejection duration, and subendocardial viability ratio). Conclusions: Our study demonstrated a correlation between serum creatinine and PWV in children with combined risk factors for atherosclerosis and probable subclinical kidney damage. Further prospective research is needed to confirm the findings, and thus the preventive role of PWV determination in paediatric nephrology.