A total of 66 children and adolescents with chronic kidney disease (CKD) (20 pre-dialysis patients and 46 chronic dialysis patients) were evaluated to address the prevalence of abnormalities in glucose and insulin metabolism and their association with cardiovascular disease. Glucose intolerance was assessed using an oral glucose tolerance test; insulin resistance was estimated by the homeostasis model assessment of insulin resistance (HOMA-IR). Carotid artery intima-media thickness (IMT) and left ventricular hypertrophy (LVH) were examined as early markers of cardiovascular disease. Thirty-four patients (7 pre-dialysis, 27 dialysis) exhibited an abnormal glucose tolerance; however, ten patients (7 pre-dialysis, 3 dialysis) were insulin-resistant. Height-specific standard deviation scores of carotid artery IMT were above normal in three of the pre-dialysis patients (15%) and in 34 of the dialysis patients (74%). LVH was present in seven pre-dialysis (35%) and 34 dialysis patients (74%). In addition, two of the pre-dialysis patients (10%) and 18 of the dialysis patients (39%) had severe LVH. The prevalence of both increased carotid artery IMT and LVH were similar in patients with or without glucose intolerance in both groups, but severe LVH was more prevalent in pre-dialysis patients with glucose intolerance (p = 0.042). The multivariate analyses showed that neither carotid artery IMT nor LVM index was predicted by serum glucose levels or HOMA-IR. In conclusion, children with CKD are at a high risk of glucose intolerance and also have a greater risk of subclinical cardiovascular disease (CVD). However, the presence of glucose intolerance does not appear to be an independent risk factor for increased carotid artery IMT or LVH.