Background/Objectives: Chronic kidney disease (CKD), the most common cause of which is hypertension and diabetes, is a recognized risk factor for cardiovascular disease (CVD). This study investigated the association between selected serum biomarkers in the context of intima-media thickness (IMT) changes, a common predictor of subsequent cardiovascular (CV) events. Methods: A total of 251 individuals were enrolled in the study, divided into groups based on the severity of CKD, the presence of CVD, and healthy controls. For this purpose, the data from the following groups of participants were analyzed: (1) end-stage renal disease (ESRD) (n = 106), (2) pre-dialyzed (PRE) (n = 48), (3) patients at stages 1 and 2 of CKD (CKD1-2) (n = 37), (4) patients with CVD and no kidney disease (CARD) (n = 28), and (5) healthy controls (HV) (n = 31). To find markers associated with elevated IMT, the each group with CVD (ESRD, PRE and CARD) was separated into two subgroups with normal and elevated IMT and compared in the relation of the studied serum biomarkers. Results: The findings identified glucose as the only marker exclusively associated with CVD. Markers uniquely linked to CKD included urea, creatinine, eGFR, total protein, CEL, neopterin, total calcium, phosphates, iPTH, sodium, iron, ferritin, and AST. All other markers reflected a combined influence of both CKD and CVD. By comparing patients with normal and elevated IMT, distinct types of CKD–CVD interactions were observed, i.e., independent (additive effects of CKD and CVD) for MPO, ALP, MMP-9, and MMP-9/TIMP-1; combined (enhanced effect due to interactions) for AOPPs and TIMP-1; and conditional (CVD impact specific to CKD patients) for AGEs, 3-NT, magnesium, UIBC, TIBC, ALT, and TIMP-1/MMP-9. However, certain markers, i.e., CML, sRAGEs, carbamylated protein groups, protein carbamylation, hsCRP, TC, HDL-C, LDL-C, TG, IL-18, klotho, FGF-23, klotho/FGF-23 ratio, potassium, NT-proBNP, and AIP were associated with both CKD and CVD, though the exact nature of their interaction could not be determined using IMT as a distinguishing factor. Conclusions: The results showed that relations between IMT and the remaining studied factors were not trivial, and most of the analyzed parameters were altered in CKD patients, especially if compared to patients with CVD but without CKD. IMT cannot be used as a universal CVD marker.
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