The aim of this study was to characterize the methodology of data collection on physical activity using accelerometry in two birth cohorts (2004 and 1993) in Pelotas, Rio Grande do Sul State, Brazil, at the 6-7 and 18-year follow-up visits, respectively. During visits to the study headquarters for a health evaluation, cohort subjects received the accelerometer to be worn on the wrist for 5 to 8 days, after which the device was retrieved at their homes. Genea and GENEActiv triaxial estimators of gravity (g) acceleration were employed. Accelerometry data were collected from 3,331 children (93.7% of those included in follow-up) and 3,816 adolescents (99% of those in follow-up). The study characterizes the data collection methodology in more than 7,000 individuals and discusses issues in its implementation. It thus provides a methodological framework aimed at helping to plan future population-based studies with the use of such technology and to improve understanding of physical activity in the context of epidemiological studies.