Gentian violet has shown carcinogenic effects after mice ingested large quantities of the substance. People rarely show side effects from external use, although you could get swelling, redness or irritation of the area to which you applied it. If your skin becomes hot and tender, you break out in sores or develop pus, particularly in areas of skin fold such as between your toes, you may have a skin infection caused by the gentian violet.
Alternative antifungal medications for fungal skin infections include nystatin, clotrimazole, ketoconazole, itraconazole and tincture of iodine. Use nystatin in a liquid form to treat fungal mouth infections, and as an ointment for skin infections; for intestinal infections, you will need to swallow the liquid. Clotrimazole and ketoconazole creams are good for skin and diaper rashes, and these are also available in both tablet and suppository forms for treating vaginal thrush.
Antibacterial alternatives for gentian violet include honey, which soldiers used 2000 years ago to treat infected wounds, and hydrogen peroxide. Use the latter to disinfect skin but avoid using it on open wounds or sores. Neosporin cream treats bacterial skin infections but is not very effective. Treat these infections with oral antibiotics for faster relief.
Researchers stain bacteria to be able to examine it under a microscope. The variety of alternative staining agents includes carmine, which stains bacteria cells red, DAPI, which is a fluorescent stain used to identify bacterial DNA, and fuchsin, a stain used to highlight muscles or collagen. Ethidium bromide colors cells that are dying, and malachite green colors bacteria for examination in the same way that gentian violet does.