Salicylic acid is the most effective wart medicine to use. It works by gradually making the wart peel off by increasing the moisture in your skin. Salicylic acid doesn’t affect the virus even though warts are caused by HPV. Salicylic acid belongs to the same class as aspirin; hence it causes a slight burn on your skin when applied. The burning side effect is expected, but tell your pharmacist or doctor if it worsens. If you are prescribed wart medication, the doctor has judged that you will benefit more than the risk of side effects. Other side effects of wart medicine include skin peeling and redness.