Warts are the skin's reaction to chronic viral infection. These raised and painful sores, often on the sole of the foot, will sometimes respond to pads and over-the-counter ointment but often need medical attention. Not all painful sores are warts. Reaction to injury, hidden slivers, and old puncture wounds can also result in painful sores. Dark brown or black warts can indicate a type of skin cancer and should be immediately examined by your physician.