This study assessed the association of breastfeeding with body composition at 30 years, among subjects who have been prospectively followed since birth in a southern Brazilian city. We also evaluated whether breastfeeding moderated the association between the rs9939609 variant in the FTO gene and adiposity. At 30 years, total and predominant breastfeeding were positively associated with lean mass index and inversely with visceral fat thickness. Among subjects breastfed for <1 month, all outcomes showed monotonically increasing values with additional copies of the A allele in the FTO genotype (rs9939609). Associations among subjects breastfed for one month or longer tended to be in the same direction but showed lower magnitude and were less consistent; for all outcomes. Interactions had p values ≤ 0.05 for body mass index, fat mass index and waist circumference. Even among young adults, breastfeeding moderates the association between the FTO variant rs9939609 and body composition.