Echinacea is one of the primary remedies for helping the body rid itself of microbial infections. It is often effective against both bacterial and viral attacks, and may be used in conditions such as boils, septicaemia and similar infections. In conjunction with other herbs it may be used for any infection anywhere in the body.

For example in combination with Yarrow or Bearberry it will effectively stop cystitis. It is especially useful for infections of the upper respiratory tract such as laryngitis, tonsillitis and for catarrhal conditions of the nose and sinus. In general it may be used widely and safely. The tincture or decoction may be used as a mouthwash in the treatment of pyorrhoea and gingivitis.

It may be used as an external lotion to help septic sores and cuts. Much research is focussing upon this plant, providing important insights into its activity and potential uses. Glycosides from the roots have mild activity against Streptococci and Staphylococcus aureus. Echinacoside was the most active with about 6 mg being equivalent to one unit of penicillin. The tincture was able to reduce both the rate of growth and the rate of reproduction of Trichomonas vaginalis, and was found to be effective in halting the recurrence of Candida albicans infection.

It seems to prevent infection and repair tissue damaged by infection, partially through inhibiting the activity of the enzyme hyaluronidase. The hyaluronidase system is a primary defense mechanism, involving connective "ground" substance, or hyaluronic acid, acting as a barrier against pathogenic organisms.

Some pathogens activate an enzyme, hyaluronidase, which once activated destroys the integrity of the ground substance. This causes the barrier to become leaky, allowing pathogens to invade, attach themselves to exposed cells, penetrate the membrane and kill the cell. The result as an inflammatory infection. Echinacea inhibits the action of hyaluronidase by bonding with it in some way, resulting in a temporary increase in the integrity of the barrier.

Fewer pathogens are able to stimulate the destruction of the ground substance. A range of constituents mediate this process, especially a complex polysaccharide called echinacin B. This anti-hyaluronidase action is involved in regeneration of connective tissue destroyed during infection and in the elimination of pathogenic organisms creating the infection.