To examine factors associated with low high-density lipoprotein cholesterol (HDL-C) levels among middle school children. HDL-C levels were the primary outcome of interest. A total of 1,104 middle-school children (mean age 11.6 years, 51.2 % female) were included in this analysis, of whom 177 (16 %) had an HDL-C level ≤40 mg/dL. More than half of those with low HDL-C were overweight or obese (62.2 %) and had greater systolic and diastolic blood pressure, triglyceride (TRG) levels, and low-density lipoprotein cholesterol levels compared with children with an HDL-C level >40 mg/dL. Among those with an HDL-C ≤ 40 mg/dL, 35 % also had body mass index ≥85 % and TRG levels ≥150 mg/dL. Exercise habits were significantly associated with HDL-C level, whereas sedentary behaviors, such as screen time, were not significantly associated with HDL-C level. Fruit and vegetable intake was also not significantly associated with HDL-C level. Children with low HDL-C levels are more likely to be overweight and to have other physiological indicators of increased cardiovascular risk. Further research is needed to determine if school-based interventions can result in long-term improvements in HDL-C. © 2013 Springer Science+Business Media New York.