Obesity in children appears to be associated with increased risk of cardiovascular and metabolic diseases later in life. Early development of insulin resistance (IR) may lead to endothelial dysfunction and increased carotid intima-media thickness (cIMT) even in childhood. We compared endothelial cell-specific molecule-1 (endocan) levels in pediatric obese patients with those in healthy controls to determine whether endocan could be used as a biological marker of complications caused by endothelial damage. In 80 obese pubertal children (44 males [M] and 36 females [F], mean age: 12.8 +/- 2.5 years), anthropometric measurements, cIMT, endocan levels, and IR indices (homeostasis model assessment of insulin resistance [HOMA-IR]) were evaluated and compared with 80 healthy pubertal patients (42M/38F, mean age: 12.3 +/- 3.2 years). High-resolution ultrasound was used to measure the cIMT. Obese children had higher levels of endocan compared with the controls (P < .001). Fasting insulin levels and HOMA-IR were also higher in obese children (P < .001 for both). In addition, obese children had an increased cIMT (P < .001). In obese children, there was a significant correlation between cIMT and HOMA-IR (beta = -1.314, P = .002) and between cIMT and endocan (beta = .483, P = .004). Measuring cIMT and endocan levels (noninvasive investigations) in obese children, together with early preventive measures, could significantly decrease morbidity and mortality in adulthood.