Body composition in infancy plays a central role in the programming of metabolic diseases. Fat mass (FM) is determined by personal and environmental factors. Anthropometric measurements allow for estimations of FM in many age groups; however, correlations of these measurements with FM in early stages of life are scarcely reported. The aim of this study was to evaluate anthropometric and clinical correlates of FM in healthy term infants at 6 months of age. Healthy term newborns (n = 102) from a prospective cohort. Weight, length, skinfolds (biceps, triceps, subscapular and the sum -SFS-) and waist circumference (WC) were measured at 6 months. Body mass index (BMI) and WC/length ratio were computed. Type of feeding during the first 6 months of age was recorded. Air displacement plethysmography was used to asses FM (percentage -%-) and FM index (FMI) was calculated. Correlations and general linear models were performed to evaluate associations. Significant correlations were observed between all anthropometric measurements and FM (% and index)(p < 0.001). Exclusive/predominant breastfed infants had higher FM and anthropometric measurements at 6 months. Models that showed the strongest associations with FM (% and index) were SFS + WC + sex + type of feeding. Anthropometry showed good correlations with FM at 6 months of age. Skinfolds sum and waist circumference were the strongest anthropometric variables associated to FM. Exclusive/predominant breastfeeding was strongly associated with FM.