Objective: Sample size and statistical power calculation should consider clustering effects when schools are the unit of randomization in intervention studies. The objective of the current study was to investigate how student outcomes are clustered within schools in an obesity prevention trial. Method: Baseline data from the Food, Health & Choices project were used. Participants were 9- to 13-year-old students enrolled in 20 New York City public schools (n = 1,387). Body mass index (BMI) was calculated based on measures of height and weight, and body fat percentage was measured with a Tanita® body composition analyzer (Model SC-331s). Energy balance-related behaviors were self-reported with a frequency questionnaire. To examine the cluster effects, intraclass correlation coefficients (ICCs) were calculated as school variance over total variance for outcome variables. School-level covariates, percentage students eligible for free and reduced-price lunch, percentage Black or Hispanic, and English language learners were added in the model to examine ICC changes. Results: The ICCs for obesity indicators are: 0.026 for BMI-percentile, 0.031 for BMI z-score, 0.035 for percentage of overweight students, 0.037 for body fat percentage, and 0.041 for absolute BMI. The ICC range for the six energy balance-related behaviors are 0.008 to 0.044 for fruit and vegetables, 0.013 to 0.055 for physical activity, 0.031 to 0.052 for recreational screen time, 0.013 to 0.091 for sweetened beverages, 0.033 to 0.121 for processed packaged snacks, and 0.020 to 0.083 for fast food. When school-level covariates were included in the model, ICC changes varied from -95% to 85%. Conclusions: This is the first study reporting ICCs for obesity-related anthropometric and behavioral outcomes among New York City public schools. The results of the study may aid sample size estimation for future school-based cluster randomized controlled trials in similar urban setting and population. Additionally, identifying school-level covariates that can reduce cluster effects is important when analyzing data.