Elevated homocysteine level is widely seen as an independent risk factor of cardiovascular disease in adults. In order to investigate the role of homocysteine in pediatric population at risk for early atherosclerosis, we studied serum homocysteine in obese children and non-obese controls. Case control study was conducted on 41 obese children comparing them with 41 healthy weight sex and age matched control group in The New Pediatric Hospital, Cairo University. Serum homocysteine level determined by ELIZA and related to carotid intima media thickness (CIMT) measured by a non invasive high resolution ultrasound and relation to other anthropometric parameters. Serum homocysteine and CIMT were all significantly elevated in obese children P value was <0.01 in both in comparison with controls. No correlation between homocysteine with CIMT and lipid profile and homocysteine correlates with BMI. There were positive significant correlation between CIMT and the anthropometric measurements including: weight, weight SDS, BMI, BMI SDS, waist circumference, hip circumference, W/H ratio, triceps SFT, triceps SFT SDS, subscapular SFT ,subscapular SFT SDS, SBP and DBP while there was no correlation between CIMT and the height . There were negative significant correlation between the CIMT and the HDL-c, but there were no significant correlation between the CIMT and total cholesterol, triglycerides and LDL-c. We concluded that serum homocysteine is elevated in obese children. Serum homocysteine level might be a characteristic for early atherosclerosis in obese children independent of other classic risk factors such as hypercholesterolemia, arterial hypertension and diabetes mellitus. Obese children are at increased risk of having thickened CIMT, especially in relation to weight, skin fold thickness (SFT), waist circumference, hip circumference, BP and HDL-c.