Although kidney transplantation significantly improves the quality of life of patients with end-stage renal disease (ESRD), the prevalence of cardiovascular disease (CVD) in kidney transplant recipients (KTRs) remains high. Atherosclerosis, post-transplantation metabolic changes, immunosuppressive therapy, and periodontitis contribute to elevated cardiovascular risk in this population. The aim of the study was to evaluate carotid intima-media thickness (IMT) as a surrogate marker of atherosclerosis and to analyze the possible risk factors for IMT in Dalmatian KTRs. Ninety-three KTRs were included in this study. Data on clinical and laboratory parameters, body composition, anthropometry, advanced glycation end-product (AGE) measurements, blood pressure, and arterial stiffness were collected. All participants underwent ultrasound examination of IMT and evaluation of periodontal status. KTRs with carotid IMT ≥ 0.9 were significantly older, had a lower level of total cholesterol, fat mass, end-diastolic velocity (EDV), and had fewer teeth. They also had significantly higher values of pulse wave velocity (PWV) and resistive index (RI). We found positive correlations between carotid IMT and duration of dialysis, age, PWV, AGE, RI, and average total clinical attachment level (CAL). The regression model showed that IMT in KTRs is associated with higher PWV, lower fat mass, and fewer teeth. The results of our study suggest that nutritional and periodontal status are associated with carotid IMT in KTRs.