Fumagillin has been used in the treatment of microsporidiosis. It is also an amebicide.
Fumagillin can block blood vessel formation by binding to an enzyme methionine aminopeptidase 2 and for this reason, the compound, together with semisynthetic derivatives, are investigated as an angiogenesis inhibitor in the treatment of cancer.
The company Zafgen conducted clinical trials using the fumagillin analog beloranib for weight loss, but they were unsuccessful.
Fumagillin is toxic to erythrocytes in vitro at concentrations greater than 10 μM.