During late infancy many infants have a protein intake, which is more than three times as high as the physiological need. Several observational studies have shown an association between a high-protein intake (>15 energy %) early in life and an increased risk of developing obesity and thereby non-communicable diseases (NCDs) later in life. This effect was supported by a recent intervention study with infant formulas with two levels of protein, showing that a higher protein intake during the first year of life resulted in a higher body mass index (BMI) at age 2 years. It is also plausible that an important reason for the slower growth in breast-fed infants is the lower content of protein in breastmilk, but other qualities of breastmilk could also play a role. A high intake of protein, especially dairy protein, stimulates the growth factors insulin-like growth factor (IGF-I) and insulin, and it has been suggested that the lower risk of NCDs in breast-fed infants is mediated through a regulation of IGF-I. A low quality of protein, as in cereal-based diets with no animal foods as often seen in low-income countries, may contribute to undernutrition, which can also result in an increased risk of NCDs later in life. In conclusion, there is some evidence that a high protein intake during the complementary feeding period is associated with increased risk of NCDs and that avoidance of a high protein intake could reduce the risk of obesity. In low-income countries, emphasis should be on providing sufficient amounts of high-quality protein to improve survival, growth and development.