Urban schools and school-based health centers (SBHCs) in low-income minority communities may be important points of intervention for overweight and obese youth. To date, little is known about the interface of overweight youth and the public health system through SBHCs. The objective of this study is to determine the prevalence, geographic distribution, sociodemographic, and comorbidity factors associated with obese status as a part of a public health system needs assessment. We conducted a cross-sectional clustered sampling utilizing prospective anthropometric measurement and chart review. Demographic, anthropometric, and medical comorbidity data were collected from 2,630 students in SBHCs in Baltimore, MD, USA. Students were geocoded to their primary residential address and assigned to a census block group using MapInfo v6.5. Demographic and comorbidity associations were analyzed using multivariable logistic regression analysis. Overall, the mean body mass index (BMI) was 25.5 (SD 6.6), and prevalence of obesity (BMI > 95th percentile) and overweight (BMI 85th-95th percentile) was 26.5% and 15.7%, respectively. Obesity was distributed among all the schools without one school being significantly more affected than others. Obese status was associated with gender, poverty, and several medical comorbidities such as asthma, high blood pressure, and disordered eating. Public health practitioners in this SBHC system appear to be faced with a greater burden of obesity than predicted by Centers for Disease Control and Prevention estimates. Given the ongoing interface with affected youth, these schools and health centers may be well situated to deliver public health obesity interventions.