A capillary sieving electrophoretic method for protein analysis and molecular weight determination was used to characterize ciders from Asturias, northern Spain. The total protein content (Bradford method) and the foam parameters (Bikerman method) were also analyzed to complete this characterization. The polypeptide profile, based on the molecular weight, together with exploratory and classification techniques, that is, principal component analysis (PCA) or linear discriminant analysis (LDA), allowed ciders to be differentiated on the basis of their foam assessment and the apple juice extraction technology used in the cidermaking process. In addition, the application of correlation analysis, that is, canonical correlations (CCA) or partial least-squares (PLS), revealed that the proteins with higher molecular weight were more relevant with respect to cider foamability. PLS analysis also provided a mathematical equation that is able to predict the stabilization time of foam from the polypeptide profile of the cider, because this is the foam parameter most influenced by these compounds.