Obesity is becoming an increasingly prevalent problem among American children. Screening for obesity associated comorbid conditions has been shown to be inconsistent. The current study was undertaken to explore patterns of ordering screening tests among obese pediatric patients. We analyzed electronic medical records (EMR) from 69,901 patients ages 2–18 years between June 1999 and December 2008. Obese children who had documented diagnoses of obesity were identified based on International Classification of Diseases, Ninth Revision codes. Screening rates for glucose, liver, and lipid abnormalities were assessed. Regression analysis was used to examine impact of patient characteristics and temporal trends were analyzed. Of the 9,251 obese diagnosed patients identified, 22% were screened for all three included obesity-related conditions: diabetes, liver, and lipid abnormalities; 52% were screened for glucose abnormalities; 30% for liver abnormalities; and 41% for lipid abnormalities. Increasing BMI and age were associated with increased rates of screening. Females and Hispanic patients were more likely to be screened. The majority of screening was ordered under “basic metabolic panel,” “hepatic function panel,” and “full lipid profile” for each respective condition. The percentages of patients screened generally increased over time, although the percentages screened for diabetes and lipid abnormalities seemed to plateau or decrease after 2004. Even after diagnosis, many obese patients are not receiving recommended laboratory screening tests. Screening increased during the study period, but remains less than ideal. Providers could improve care by more complete laboratory screening in patients diagnosed with obesity.