Intra-individual variability (IIV) refers to relatively stable differences between individuals in the degree to which they show behavioral fluctuations over relatively short time periods. Using temperament as a conceptual framework the structure, stability, and biological roots of IIV were assessed over the first year of life. Biological roots were defined by maternal and infant nutrition. The sample was 249 Peruvian neonates, followed from the second trimester of pregnancy through the first 12 months of life. Maternal anthropometry, diet, iron status, and fetal growth were assessed prenatally. Neonatal anthropometry and iron status were assessed at birth. Degree of exclusive breastfeeding was assessed at 3 and 6 months, infant anthropometry was assessed at 3, 6, and 12 months, infant dietary intake was assessed at 6 and 12 months and infant iron status was tested at 12 months. Individual differences in IIV at 3, 6, and 12 months were derived from a residual standard deviation score based on infant behaviors measured using the Louisville Temperament Assessment Procedure. Principal components analysis indicated that individual differences in IIV were defined by two components at 3, 6, and 12 months. There was modest stability between IIV components assessed at 3 and 12 months. Reduced levels of IIV at 3 months were predicted by higher maternal weight and higher fetal weight gains in the first and second trimesters of pregnancy. Higher levels of IIV at 3 months were predicted by higher levels of maternal hemoglobin during pregnancy and higher levels of neonatal ferritin.