The purpose of this study was to assess differences across household food security levels in obesity, central adiposity, and metabolic syndrome among children 12 to 18 years of age. Data for 7,435 adolescents between the ages of 12-18 years were downloaded from the National Health and Nutrition Examination Survey (NHANES)1999-2006. Food security status was assessed using the USDA food security Survey Module. Body mass index (BMI) data were classified into CDC weight categories, and central adiposity was identified based on the International Diabetes Federation (IDF) cutoff for the 90th percentile. Differences were assessed using analysis of covariance and logistic regression, controlling for age, gender, and race. Nearly two-thirds (75.9%, n = 5,643) of the sample were from high food secure (HFS) households, while 7.1% (n = 528), 10.8% (n = 803) and 6.1% (n = 454) were from households that were marginally food secure (MFS), low food secure (LFS) and very-low food secure (VLFS), respectively. There were no significant differences in mean BMI-for-age percentiles by food security status (p = 0.087); however, MFS (44%, Odds Ratio: 1.44 [1.12-1.87]) and LFS (44.0%, Odds Ratio: 1.44 [1.13-1.84]) were significantly more likely to present with a BMI >85th percentile than HFS households. Adolescents from HFS households had significantly lower mean central obesity than those from MFS and LFS households (p < 0.001). MFS (52%, Odds Ratio: 1.52 [1.08-2.15]), LFS (42.0%, Odds Ratio: 1.42 [1.11-1.80]) and VLFS (51%, Odds Ratio: 1.51 [1.10-2.08]) were significantly more likely to present with central adiposity than those from HFS households. Only those from HFS households had significantly higher HDL than children from LFS households in our study (p = 0.019). There were no significant differences in blood glucose, triglyceride, LDL, systolic blood pressure, diastolic blood pressure, and total cholesterol by food security category. Food insecurity appears to be a risk factor for central obesity and is associated with low HDL levels among U.S. children.