The organisms causing fungal infections of the toes thrive in warm, moist areas, such as showers and swimming pools. These dermatophytes can cause athlete's foot, affecting the toes, and onycomycosis, affecting the toenail. Athlete's foot is typically treated for 2 to 6 weeks, but onychomycosis may require 9 to 18 months of treatment. Diabetics and those with serious medical conditions should check with their physician before using over the counter medications.

Clotrimazole

Sold as Lotrimin AF and Desenex, clotrimazole is available over the counter for the treatment of athlete's foot and as FungiCure Intensive Anti-Fungal Treatment for treating onychomycosis. Clotrimazole should be applied twice a day, wearing gloves or using an applicator. Clotrimazole should only be used externally. Side effects, including burning or itching, are generally minimal.

Miconazole

Miconazole is another over the counter medication for fungal infections of the toes. For athlete's foot, it is sold as Monistat-Derm cream. For toenail infections, it is sold as Humco Miranel AF Anti-Fungal Treatment and Clearly Confident AF Cream. Miconazole should be applied twice a day. According to Drugs.com, it should not be used by pregnant or breastfeeding women and children under 2. Side effects include itching and a rash. It is for external use only.

Terbinafine

Terbinafine is a prescription strength over the counter medication. Terbinafine, sold as Lamisil and Lamisil AT, is not for use in children under 12. Terbinafine is applied externally twice a day. Terbinafine is considered to be the most effective treatment for a fungal infection between the toes. It is not effective for onychomycosis. According to Drugs.com, there can be interactions with some prescription medications, so terbinafine should be used under a doctor's care.

Tolnaftate

For athlete's foot, tolnaftate is sold as Tinactin and Aftate as a cream, gel, spray and powder. For onychomycosis, it is sold as Mycocide NS and Pro Clearz solutions. Tolnaftate works by inhibiting the growth of the fungi. It is applied twice daily and is for external use only. The side effects include irritation or itching.

Undecylenic Acid

Undecylenic acid is sold over the counter as Tineacide and FungiCure Anti-Fungal Liquid. It works by inhibiting fungal growth and is effective in the treatment of athlete's foot. It is applied externally twice a day. According to Drugs.com, undecylenic acid should not be used by pregnant or breastfeeding women or by diabetics. Side effects include stinging and itching. Shortness of breath or swelling of the mouth, lips or tongue require immediate medical attention.

Tea Tree Oil

Tea tree oil is an herbal medication used for the treatment of athlete's foot and onychomycosis. Tea tree oil a derivative of the leaves of the Melaleuca alternifolia. According to Drugs.com, it has not been evaluated by the FDA for safety or effectiveness. It should not be used without consulting a doctor because its interactions and side effects are not all known. Tea tree oil is sold as DiabetiDerm Toenail, Foot Anti-fungal Cream, Flexitol Maximum Strength Anti-fungal Nail Fungus Liquid and the homeopathic medication, Zetaclear.