IMPORTANCE: The incidence of obesity is rising in the United States and has been linked to Obstructive Sleep Apnea (OSA) even in young children. Understanding the role that obesity and OSA play in alterations in metabolic variables that can lead to serious health issues is essential to the care and counseling of affected children. OBJECTIVES: To evaluate the association of alterations in metabolic variables, including insulin resistance, to OSA in young, obese children. DESIGN: Retrospective, case-control series. SETTING: Tertiary care children's hospital. PARTICIPANTS: Obese children aged 2-12 years who had undergone overnight polysomography and routine laboratory testing for lipid levels, fasting glucose, and insulin from January 1, 2006 to December 31, 2012 were identified from a TransMed Bio-Integration Suite and Epic's clarity database search. RESULTS: A total of 76 patients were included for analysis. Forty-three (56.6%) were male, and the mean age was 8.3+/-2.5 years (range, 2.4-11.9 years). The mean body mass index (BMI) z score was 2.8+/-0.75 (range, 1.7-6.3), and all patients were obese (BMI z score>95th percentile). Twenty two patients (28.9%) had an apnea-hypopnea index (AHI) <1/h (no OSA), 27 (35.5%) an AHI>/=1<5/h, 12 (15.8%) had an AHI >/=5<9.99/h, and 15 (19.7%) had an AHI>/=10/h. There was no significant difference in total cholesterol, triglycerides, high and low density lipoprotein levels, systolic and diastolic blood pressure in those patients with or without OSA. Fasting insulin, blood glucose, and homeostasis model assessment (HOMA) were significantly higher in patients with OSA compared to those with no OSA (p<0.01). AHI correlated to alterations in insulin as well as glucose homeostasis on multivariate analysis. Results from logistic regression analysis showed that fasting insulin (p<0.01), and HOMA (p<0.01) predicted severe OSA independent of age, gender, and BMI z score in these patients. CONCLUSION: Metabolic alterations in glucose and insulin levels, known to be associated with obesity and increased risk for cardiovascular disease, appear to relate to the severity of OSA in young children.