Epidemiological studies have supported the hypothesis that dietary calcium intake is protective for adiposity. This study aimed to estimate the association of dietary calcium with adiposity indicators during adolescence. This is a cohort study with high school adolescents (n = 962) from selected schools of the Metropolitan Region of Rio de Janeiro, Brazil, which were followed from 2010 to 2012. Calcium intake was assessed by a validated self-reported food frequency questionnaire. Cross-sectional and longitudinal analyses of dietary calcium intake were performed regarding body mass index (BMI), waist circumference (WC), body fat percentage (%BF), fat mass (FM), fat-free mass (FFM), fat mass index (FMI), and fat-free mass index (FFMI). The analysis of variance was used for cross-sectional analysis with baseline data and linear mixed models applied to assess changes across the follow-up. At baseline, BMI, %BF, fat mass, and FMI (p for trend < 0.05) had lower means at the highest quintile of calcium intake whereas FFM and FFMI had higher means (p for trend < 0.05), especially for boys. During follow-up, boys had decreased FMI at the 4th and 5th quintiles of calcium intake (p < 0.05); among girls, only WC was significantly lower at the 4th quintile than in the 1st. These results support the hypothesis that low calcium intake increases adiposity among adolescents.