Last Updated on March 17, 2025
Penile agenesis or aphallia means an absence of formation of the penis. It is a rare condition occurring in 1 in 30 million births and results from a development failure of the genital tubercle during the fourth week of embryogenesis.
The genital tubercle is the embryonic progenitor mesenchymal tissue forming penis in man and clitoris in the woman.
It is formed through tissue budding mesenchymal tissue underneath genital ectoderm next to cloacal membrane.
[The term aphallia is used to denote failure of formation of the penis as well as a failure of formation of the clitoris.
The more common use though refers to the absence of a penis in males.]
The scrotum is normal and contains normal testicles. Patients are otherwise normal 46, XY males
The urethra passes generally into the rectum.
The classic treatment of penile agenesis was to assign the child to female gender by cutting the gonads and recreating vagina along with drug treatment to induce breast growth.
But modern treatment has seen a shift towards phallus reconstruction so that the patients grow as boys. This also saves the patient and the family psychological issues and conflicts that they face with female gender assignment.
The urethra might open in rectum [more common] located in the perineum inside a skin tag, resembling a foreskin.
Aphallia is reported more in diabetic mothers.

Associated conditions
Patient of penile agenesis may have many associated conditions. Some of them are serious to cause early deaths.
Following conditions have been reported by different authors
- Imperforate anus
- Anal stenosis
- renal agenesis
- Renal dysplasia
- Cystic kidney
- Horseshoe kidney
- Prostate agenesis. Of
- Neurological disorders
- Annular pancreas
- Clubfoot
- Cardiac Problems
- Right lung agenesis
- Spinal disorders like sacral agenesis
Pathophysiology of Penile Agenesis
Aphalia results from a development failure of the genital tubercle during the fourth week of embryogenesis.
The genital tubercle is the embryonic progenitor mesenchymal tissue forming penis in male and clitoris in the female.
SRY gene is the sex-determining transcription factor on Y chromosome. This gene expression leads to gonad development as male gender and Anti-Mullerian Hormone is secreted by developing testicle’s Sertoli cells so that internal and external genital system is inclined to the male gender.
In addition to SRY gene, the external genital system develops as cauda from septum whose development basically depends on androgen (testosterone) and similar to other septum organs, epithelial-mesenchymal interaction plays the key role in their development.
The urine in these patients passes from the front part of the rectum.
Phallus agenesis has been classified into three types as presphictric, postsphictric and urethral atresia depending on the urethral opening position
Because they suffer from several disorders, many patients die a few days after birth. This is seen especially in those where the urethral opening is seen.
Differential Diagnoses
- Severe microphallus
- Epispadias or hypospadias
- Intrauterine penis amputation
Assessment of Child with Penile Agenesis
The newborn is evaluated by a multidisciplinary team of surgeons, radiologists, geneticists, psychologists, endocrinologists, and pediatricians.
The diagnostic evaluation consists of procedures to find associated conditions.
These include an ultrasound of kidneys, MRI of the pelvis, retrograde urethrogram, a distal colonogram through the mucous fistula [in imperforate anus] and other investigations as dictated by individual case.
Management of Penile Agenesis
The management of aphallia is a challenge. Quite a lot of these neonates die early due to associated life-threatening reasons. Those who survive, their genitals reconstruction is taken into account.
In the past, the management consisted of assigning the child a female gender probably because of limited surgical options and operational ease.
But this results in psychological and sexual identity issues [gender dysphoria]
Because of this, there are increased efforts to made to reconstruct genitals for the male gender. It must be noted that unlike other chromosomal-related conditions, infants with penile agenesis have completely normal testicular hormone function, making them, to all intents and purposes, male.
Making a choice is one of the most challenging conditions.
First and foremost is separating the urinary system from the digestive system, which has to be done as soon as possible.
In imperforate anus, it requires colostomy, vesicostomy and urethral passage to the perineum.
Gender Reassignment
If reassignment has to be done, it should be done in the neonatal period is ideal as gender awareness begins around 18 months after birth. It becomes well established by 2.5 years of age.
However, the difficulty of creating a penis left the only rational choice to create female genitalia.
It requires bilateral orchiectomy and the creation of a neovagina, which is most frequently performed with a sleeve of sigmoid colon. Acting early to prevent male gender imprinting is critical. Removal of the testicles is usually carried out as soon as practicable. Vaginoplasty is then carried out soon after.
At or around puberty, estrogen therapy for breast and the other gender features development in women are suggested.
In addition, sex reassignment in the neonatal period with early orchidectomy may have the advantage of preventing the postnatal testosterone surge and central nervous system testosterone imprinting which are important to subsequent gender identity
Neophallus Construction
Recently there is an increased trend to save the boyhood. This requires the creation of neophallus.
The cases with an associated imperforate anus and recto-urethral fistula require an urgent colostomy and a vesicostomy [this needs to be done irrespective of gender selection]
The urethra is shifted to between the scrotal folds which are preserved for subsequent genital reconstruction.
Phalloplasty has to be conducted at puberty time.
However, phalloplasty technique and complete urethroplasty using a quadrangle lower abdominal flap can bridge the interval between childhood and adolescence until a more definitive procedure can be undertaken
Phalloplasty procedure in adolescents and adults is the microvascular transfer radial forearm flap and use of oral or bladder mucosa for the urethroplasty.
References
- Evans JA, Erdile LB, Greenberg CR. Agenesis of the penis: patterns of associated malformations. Am J Med Genet. 1999;84:47–55.
- Goenka A, Jain V, Sharma R, Gupta G, Bajpai M. MR diagnosis of penile agenesis: is it just absence of a phallus? Pediatr Radiol. 2008;38:1109–12. doi: 10.1007/s00247-008-0910-1.
- Bateman C. World’s first successful penis transplant at Tygerberg Hospital. S Afr Med J. 2015;105:251–2.