Protein is the most satiating macronutrient, increasing secretion of gastrointestinal hormones and diet induced thermogenesis. In phenylketonuria (PKU), natural protein is restricted with approximately 80% of intake supplied by a synthetic protein source, which may alter satiety response. Casein glycomacropeptide (CGMP-AA), a carbohydrate containing peptide and alternative protein substitute to amino acids (AA), may enhance satiety mediated by its bioactive properties. Aim: In a three-year longitudinal; prospective study, the effect of AA and two different amounts of CGMP-AA (CGMP-AA only (CGMP100) and a combination of CGMP-AA and AA (CGMP50) on satiety, weight and body mass index (BMI) were compared. Methods: 48 children with PKU completed the study. Median ages of children were: CGMP100; (n = 13), 9.2 years; CGMP50; (n = 16), 7.3 years; and AA (n = 19), 11.1 years. Semi-quantitative dietary assessments and anthropometry (weight, height and BMI) were measured every three months. Results: The macronutrient contribution to total energy intake from protein, carbohydrate and fat was similar across the groups. Adjusting for age and gender, no differences in energy intake, weight, BMI, incidence of overweight or obesity was apparent between the groups. Conclusion: In this three-year longitudinal study, there was no indication to support a relationship between CGMP and satiety, as evidenced by decreased energy intake, thereby preventing overweight or obesity. Satiety is a complex multi-system process that is not fully understood.