Multifaceted community interventions directed at improving food environments are emerging, but their impact on dietary change and obesity prevalence has not been adequately documented. The Healthy Communities Study (HCS) is seeking to identify characteristics and combinations of programs and policies that are associated with children's diets and obesity-related outcomes in various types of communities across the U.S. The purpose of this paper is to describe the methods used in 2013-2015 in the HCS to assess dietary intake, school nutrition environments, and other nutrition-related behaviors. The conceptual framework of the HCS is based on the socioecological model and behaviors shown in previous studies to be related to obesity in children guided selection of domains. Nine domains were identified as essential measures of nutrition in the HCS: (1) intake of selected foods and beverages; (2) food patterns and behaviors; (3) social support; (4) home environment; (5) school environment; (6) community environment; (7) breastfeeding history; (8) household food insecurity; and (9) dieting behaviors and body image. Children's dietary intake was assessed using a dietary screener and up to two automated 24-hour recalls. Dietary-related behaviors were assessed by a survey administered to the parent, child, or both, depending on child age. School nutrition measures were obtained from a combination of school staff surveys and researcher observations. Information from these measures is expected to contribute to a better understanding of "what is working" to improve the dietary behaviors that are likely to prevent obesity and improve health in children.