The purpose of this study was to evaluate the shelf-life stability (6 months) of model infant formula with whey protein hydrolysates or peptidic fractions as carrageenan replacers. Whey protein hydrolysates were prepared with trypsin and followed by ultrafiltration of the hydrolyzed mixture, and peptidic fractions were isolated from the ultrafiltered tryptic hydrolysate by anion- or cation-exchange chromatography. The stability of the model infant formula was evaluated using a stratification method based on fat content differences between the top and bottom strata of the samples. With protein hydrolysate-based formulations, the creaming rate of the fat in the product was slightly higher than in the standard formulation (with carrageenan), which is indicative of lower storage stability. The addition of cationic fractions to model infant formula also resulted in lower product stability, whereas the fat creaming rate was retarded in anionic fraction based formulations. The physicochemical characteristics of certain peptides combined with the reported high emulsifying properties of peptidic sequences found within these fractions may account for their ability to act as carrageenan replacers.