Background: This study sought to examine the associations of traditional and non-traditional cardiovascular risk factors with carotid intima-media thickening and plaque in peritoneal dialysis (PD) patients. Methods: A cross-sectional study was performed in 147 PD patients with carotid intima-media thickness (IMT) and plaque assessed by B-mode ultrasonography and fasting blood collected for biochemical measurements. Results: On univariate analysis, age, smoking history, fibrinogen, C-reactive protein (CRP), adiponectin, fetuin-A, lipoprotein(a) and diastolic blood pressure were associated with carotid IMT while age, smoking history, diabetes, CRP and diastolic blood pressure were associated with carotid plaque. Using multivariate analysis, elevated CRP (p = 0.015) and serum calcium (p = 0.022) were associated with carotid plaque but not with IMT. CRP and serum calcium were synergistically associated with carotid plaque in that those with CRP > median and serum calcium > median showed the highest prevalence of carotid plaque than either factor alone (p = 0.003). Conclusions: An elevated CRP appeared to be a better biomarker of presence of carotid plaque than intima-media thickening. Furthermore, CRP and serum calcium showed synergistic association with presence of carotid plaque. However, our study was limited by the cross-sectional design and baseline laboratory abnormalities were inevitably confounded by the treatment already given, resulting in difficulty to distinguish cause and effect relationship. Nevertheless, these observations warrant further investigation as it may potentially have important implications on differentiating therapeutic strategies for reducing carotid IMT and plaque progression in PD patients.