If you've never had sex, little white bumps on the shaft of the penis may be pimples, a skin cyst, or ingrown hairs. These are common and they're nothing to worry. Feb 21, - They usually aren't harmful or a cause for concern. Cysts usually don't appear on the penis, but it is possible. In many cases, penile cysts won't cause any pain or discomfort. Cyst-like bumps may be a symptom of a sexually transmitted disease (STD).Cyst or STD-related bump? · Cyst types and causes · Diagnosis · Treatment.