The aim of this study was to develop instructions for using accelerometers to measure physical activity in Brazil. This manuscript is a review and synthesis of scientific papers that have used accelerometers for objective physical activity assessment in different age groups as well as studies providing directions for using activity monitors in large-scale studies. In this study, we present instructions for the pre-data collection (selection of monitor; unit calibration, firmware update, pilot study, protocol definition), data collection (monitor distribution, contacting participants, monitor return) and post-data collection (data processing, transformation and interpretation) phases. We describe procedures for facilitating decision making related to using accelerometers, as well as for obtaining valid and reliable accelerometer physical activity data. This set of instructions is an initiative of a group of physical activity researchers with the purpose of contributing to methodologically advance the field of objective physical activity measurement in Brazil. The current set of instructions intend to facilitate the standardization of procedures for collecting physical activity data with accelerometers in Brazil and, thus, for ascertaining future comparability of data collected in different studies.