Low endotoxin fucan compositions comprising a therapeutically effective, medically acceptable fucan in a composition comprising less than about 0.2, 0.18, 0.1, 0.01, 0.001, or 0.0005 endotoxin units (EU) per milligram of the fucan are disclosed. Methods and systems for removing or reducing the amount of endotoxins from a starting fucan composition are also disclosed.