A method of preparing an amniotic membrane extract including the steps of obtaining a healthy amniotic membrane from a pregnant mammal, such as a pig, cow, horse or human, homogenizing the membrane to obtain a homogenate solution, freezing the homogenate solution, and lyophilizing the frozen homogenate solution to dryness is disclosed. Preferably, the lyophilized homogenate is pulverized to a powder. The lyophilized homogenate is then reconstituted before use, e.g., in a liquid, such as a balanced salt solution or fresh amniotic fluid, or in another substance, such a gel, an ointment, a cream or a soap, depending on the intended use. Also disclosed is a pharmaceutical composition prepared according to the method of the invention, for prophylaxis and / or treatment of a disease or condition, especially of the eye or the skin. Exemplary pharmaceutically acceptable carriers for the composition of the invention include an ophthalmic solution for eye drops, a gel, an ointment, an emulsion, a cream, a powder and a spray.