The invention provides a method of separating a first and a second set of fullerenes in a fullerene mixture. In the method of the invention, a stable fullerene cation is formed of one of the first or the second set of fullerenes. The fullerene cation is then separated from the other set of fullerenes. Optionally, the fullerene cation may be returned to its neutral state. The method of the invention is particularly useful for the purification and separation of endohedral fullerenes from empty fullerenes. However, the method may be applied to the purification of a broad range of endohedral and empty fullerene materials.