The antibiotic fumagillin with amebicidal and fungicidal effects isolated from Aspergillus fumigatus is the only presently known agent for the treatment of life threatening serious microsporidiosis occurring in patients with AIDS. Fumagillin and its degradation products were measured by HPLC at given time intervals after storage under defined conditions (temperature, relative humidity). Significant degradation took place even in samples stored in freezer; therefore fumagillin drug substance should be stored below -60 degrees C. Light also induced a degradation process in fumagillin, thus it is proposed to be stored and transported in brown glass.