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The Healthy Communities Study is one of the largest studies to assess the relationship between characteristics of community programs and policies to prevent childhood obesity and obesity-related outcomes. The purpose of this paper is to describe the protocol that was developed for collecting the anthropometric data for the study and the procedures for analyzing the data. Data were collected from 2013 to 2015 and analyses will be completed by mid-2016. During in-home visits, Healthy Communities Study staff collected height, weight, and waist circumference measurements from child participants and height and weight measurements from adult participants. The protocol for obtaining these measurements was adapted from the protocol used by the National Health and Nutrition Examination Survey, with modifications to accommodate assessments conducted in homes rather than in a Mobile Examination Center. In addition to anthropometric data from in-home visits, the Healthy Communities Study collected retrospective height and weight measurements from the medical records of child participants. These data were used to calculate trajectories of BMI and BMI z-scores. The study implemented procedures for ensuring the accuracy of the in-home measurements and abstracted medical data. These procedures included automatically checking the ranges on entered data, reviewing data for end-digit patterns, and abstracting selected medical records using two independent abstractors to assess agreement. The collection of longitudinal height and weight measures will allow researchers to address several pressing questions related to how characteristics of community programs and policies are associated with obesity-related outcomes among children.