An in-depth analysis of the donkey milk protein profile has been performed in this study. The interest was focused on the milk proteins considered safe for the prevention and treatment of various disorders in human. Since donkey milk supply is related to its seasonal availability during the year, in this study were evaluated the effects of different thermal treatments on the protein fractions of donkey milk. The results obtained in fresh, frozen, powdered and lyophilized donkey milk showed different values in total proteins, caseins, whey proteins and lysozyme content. This study demonstrated the possibility of using lyophilization in order to maintain the nutritional characteristics of donkey milk. The article presents some promising patents on the effects of thermal treatments on donkey milk nutritional characteristics.