Sep 21, · I have blood clots coming out of my penis & alot of blood when i go number 2, whats wrong? There can be many causes of blood clots coming from penis.5/5. i was changing my babies diaper and i was cleaning him up and noticed he had blood coming from the head of his penis i checked his diaper and there was none. Nov 07, · there are small drops of red blood coming from his penis after he pees. I took him to the dr who thought it was kidney stones and sent him for an ultrasound and the ultrasound came back fine - no problem with the kidneys.