They may be just harmless spots, but some times, skin pigmentation in covered areas can be due to adrenal problems. There may be other reasons as well. So, it is advised to consult a good dermatologist and get his expert opinion.
Most of the time, the kind of skin color changes you describe are harmless rashes or other minor skin-based irritations; however, sometimes they can indicate that there may be something else going on, of which the discoloration is just a sign. Why not take the question up in person with a doctor, just to be sure? He (or she) can take a look and give a more definitive answer; assuming that it is nothing to worry about, you then will have peace of mind if more emerge. Also, remember o keep your penis in good overall health through the use of a quality penis vitamin cream (health professionals recommend Man1 Man Oil). A cream with a powerful antioxidant, such as alpha lipoic acid, is best.
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