It is extremely rare for boys to be born without a penis. In fact, it occurs in less than 1 in 30 million male births.[i] The disorder is called penile agenesis (also called aphallia – meaning lack of a phallus or penis). Click HERE to see an example of aphalia. In this disorder, the penis was not formed during development. Many of these babies have other abnormalities; however, some simply are missing the penis but have fully developed scrotum and testicles. It is possible for reconstructive surgery to be performed in some of these cases.[i]
The leading cause of “not having a penis” occurs in obese boys and men. For many obese males, layers of fat can accumulate on the pubic bone and cover the base of the penis making it appear shorter. In cases where there are significant layers of pubic fat, the entire penis may become completely “buried” in the fat and not visible at all – this is called an “inconspicuous penis.” In some men, the layers of fat are only a couple of inches deep so an erection will extend out of the fat layer and allow for sexual activity (although sometimes limited). However, in extreme cases the fat layers may be so thick that an erection may not extend far enough past the fat to be visible, let alone allow the man to engage in sexual activity. Weight loss is recommended as a first line treatment for obese men who have some or all of their penis buried in layers of fat.
[ii] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4601949/ (3/20/17)