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The increased incidence of allergies to cow’s milk proteins (CMP) in newborns enhanced the production of infant formula based on either soy proteins and/or hydrolysates of CMP. These formula, although having a good nutritional value, can be affected by the presence of peptides with a size stimulating the immunological response in predisposed subjects and/or an unpleasant taste for the infant consumers. Recent clinical studies indicated that patients with CMP allergy and also intolerant to these formula, showed a high tolerance towards the donkey milk, due to its greater quantitative similarities to human milk than cow’s milk. Specifically, although the mechanism of this tolerance has not yet been clarified, it is reasonable to hypothesize that the reduced allergenic properties of donkey milk can be related to structural differences of its protein components with respect to cow’s milk. At present, compared with cow’s milk, the characterization of donkey milk proteins (whey proteins and mainly caseins) is at a relatively early stage of progress, and only limited data are related to their heterogeneity. In this PhD thesis the complexity and specifically the qualitative and quantitative heterogeneity of donkey milk proteins of 77 animals reared in Italy was investigated using a proteomic approach. This analytical procedure for structural analysis of protein fractions is based on the combination of highly efficient separation techniques, such as one-dimensional electrophoretic techniques (PAGE pH 8.6, UTLIEF, PAGE-SDS) or, more efficiently, the two dimensional (2-DE) electrophoresis, coupled either to Coomassie Brilliant Blue staining or immunospecific staining with polyclonal antibodies, to chromatography analysis (RP-HPLC), interfaced to structural Mass Spectrometry analysis (LC/ESI/MS, MALDI/TOF/MS, ESI q-TOF/MS). For donkey caseins, these combined methodologies allowed the contemporary identification of the four casein fractions (αs1-, αs2-, β- and κ-CN) in donkey mi