Background Most population-based studies from Latin America have used questionnaires to measure physical activity (PA) and sedentary behaviors (SB). Low reliability and validity of the questionnaires has limited the capacity to examine associations between PA and health. The purpose of this study was to compare self-reported and accelerometer-measured PA and SB and their associations with body composition in Latin American countries. Methods Data were obtained from the Latin American Study of Nutrition and Health (aged 15-65 years), collected from September 2014 to February 2015. PA and SB were assessed using the International Physical Activity Questionnaire (long version) and the Actigraph GT3X+ accelerometer. Outcomes of interest included: body mass index (BMI), waist (WC) and neck circumference (NC). We used the Pearson and intraclass correlation coefficient, Bland-Altman plots, and multilevel linear regression models. Results Mean moderate-to-vigorous physical activity (MVPA) by accelerometer and IPAQ were 34.4 min/day (95% CI: 33.4 to 35.4) and 45.6 min/day (95% CI: 43.2 to 48.1), respectively. For SB (accelerometer and IPAQ) the means were 573.1 (95% CI: 568.2 to 577.9) and 231.9 min/day (95% CI: 225.5 to 238.3). MVPA, measured by the accelerometer was negatively associated with BMI (β = -1.95; 95% CI: -2.83 to -1.08), WC (β = -5.04; 95% CI: -7.18 to -2.89) and NC (β = -1.21; 95% CI: -1.79 to -0.63). The MVPA estimated through IPAQ was not significantly associated with any of the three outcome variables. SB, measured by the accelerometer, was positively associated with BMI (β = 0.26; 95% CI: 0.08 to 0.44) and WC (β = 0.48; 95% CI: 0.13 to 0.91). SB estimated through IPAQ was positively associated with NC only. Conclusions Low correlation coefficients were observed for accelerometer-derived and IPAQ-reported estimates of PA and SB. Caution is advised when making comparisons between accelerometer-measured and self-reported PA and SB. Further, studies examining associations between movement and health should discuss the impact of PA and SB measurement methodology on the results obtained.