Journal of Clinical Neonatology

: 2022  |  Volume : 11  |  Issue : 4  |  Page : 230--232

A rare case of aphallia associated with urethral atresia and multiple renal anomalies

M Shafiq Ahamed, KK Neethu 
 Department of Pediatrics, Government Medical College, Thrissur, Kerala, India

Correspondence Address:
M Shafiq Ahamed
Assistant Professor in Pediatrics, Government Medical College, Thrissur, Kerala


Aphallia, or penile agenesis, is an extremely rare congenital anomaly, resulting from the failure of the genital tubercle to develop normally during the early period of embryogenesis. We present the case of a baby born at term by normal vaginal delivery to a primi mother with an uneventful antenatal history, except for oligohydramnios detected in the third trimester. Examination of the baby revealed an absence of phallus and external urethral meatus, normally descended testes, a normal scrotum, and a normally positioned patent anal orifice. Subsequent workup of the baby by radiological studies revealed a malrotated right kidney in the midline, multicystic renal dysplasia of the left kidney, and urethral atresia.

How to cite this article:
Ahamed M S, Neethu K K. A rare case of aphallia associated with urethral atresia and multiple renal anomalies.J Clin Neonatol 2022;11:230-232

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Ahamed M S, Neethu K K. A rare case of aphallia associated with urethral atresia and multiple renal anomalies. J Clin Neonatol [serial online] 2022 [cited 2023 Jan 30 ];11:230-232
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Full Text


Aphallia is an extremely rare congenital genitourinary anomaly with an estimated incidence of about one in 30 million live births.[1] Aphallia is believed to result from the failure of the genital tubercle to develop normally during the early period of embryogenesis.[2]

More than 50% of the cases of aphallia are associated with other anomalies, that include developmental defects of the caudal axis, and genitourinary and gastrointestinal anomalies.[3] The site of urethral opening in cases of penile agenesis differs; it may open anywhere along the perineal midline raphe, but most commonly opens onto the anterior wall of the anal verge.[4]

Here, we report a case of aphallia associated with urethral atresia, malrotation of the right kidney, and multicystic dysplasia of the left kidney.

 Case Report

A neonate was born at term to a 26-year-old primi mother hailing from a tribal family. The parents were unrelated and healthy. Ultrasonogram revealed oligohydramnios and possible hydroureteronephrosis during the third trimester. An emergency Caesarean section was done in view of oligohydramnios and decreased fetal movements.

The baby was noted to have an absent penis and absent external urethral meatus, and hence referred to our hospital shortly after birth. The baby was received in our hospital at 5 hours of life. There was no family history of any genito-urinary anomalies.

Physical examination showed an active, pink, and euthermic baby. The vital signs were recorded to be normal. There was no facial dysmorphism. The abdomen was soft and distended. A ballotable mass was palpable on the left side of the abdomen. Local examination of external genitalia showed an absence of penis and external urethral meatus. The scrotum was normal with a median raphe, and normal rugosities. Both the testes were descended and palpable in the scrotal sac. The anal orifice was patent and normally positioned, with no perianal urethral opening identified [Figure 1].{Figure 1}

Postnatal ultrasonography showed moderate hydroureteronephrosis of the right kidney, and multicystic dysplasia of the left kidney, and was unable to visualize the course of the urethra. A thick-walled urinary bladder was visualized, with bilateral testes in the scrotum. The pelvis showed typical anatomy, and no female internal organs were visualized. Karyotyping revealed a normal male karyotype (46 XY).

DMSA scintigraphy done at 6 months of life showed the right kidney to be malrotated (with renal pelvis facing downwards) and in the midline; the left kidney was not visualized [Figure 2]. Cystourethrogram suggested a normally filling bladder with no extra-vesical leakage of contrast [Figure 3].{Figure 2}{Figure 3}

The default plan before reconstruction was to perform an interim urinary diversion (vesicostomy) and place the patient on prophylactic antibiotics to prevent urinary tract infection. On follow-up at 1 year of age, the infant is voiding through vesicostomy, and there has been no urinary tract infection so far. The child can feed well, and has achieved satisfactory weight gain so far.


Early in the 4th week of gestation, the proliferation of mesenchyme around the cloacal membrane results in the formation of a pair of swellings called cloacal folds. Cranial to the cloacal membrane, the cloacal folds unite to form the genital tubercle. Under the influence of testosterone secreted by Leydig cells of fetal testes and Dihydrotestosterone formed by 5-alpha reductase activity, the genital tubercle enlarges and becomes cylindrical to form the phallus (primitive penis). Further enlargement of the phallus forms the penis.

Aphallia occurs due to an impairment in mesenchymal proliferation, resulting in the failure of the genital tubercle to develop normally. The urethra may open at any point along the perineal midline raphe but most commonly opens onto the anterior wall of the anal verge. An insult to the early stages of development also affects the cloacal eminence, leading to proximal urethrorectal communication and associated urogenital anomalies. On the other hand, an insult later on results in the urethra opening distally at the anal verge without associated urogenital anomalies.[5] There are also reports of cases of aphallia presenting with the absence of the urethra and a blindly-ending urethra.[6],[7] In our case, there was no external urethral opening.

Aphallia may occur alone or in association with other congenital anomalies. The associated anomalies include renal agenesis, dysplastic kidneys, vesicoureteral reflux, cryptorchidism, trachea esophageal fistula, ventricular septal defect, single umbilical artery, anorectal or musculoskeletal anomalies.[8]

Skoog and Belman classified aphallia based on the position of urethral opening in relation to the anal sphincter as postsphincteric, presphincteric, and urethral atresia. They observed that the more proximal the urethral meatus, the greater the chance of mortality and higher the incidence of other anomalies. The postsphincteric group had the highest survival rate (87%) and lowest incidence of other anomalies, followed by presphincteric group (36% mortality); 12% had urethral atresia (100% mortality).[9] Our case belonged to the third group, and was associated with multiple renal anomalies.

The conventional method of management of penile agenesis was to assign female gender to the patient, and perform multi-staged reconstructive procedures. Recently, the concerns related to the long-term psychological effects of gender conversion have led to recommendations that patients with aphallia should be raised based on their karyotype and hormone production. The decisions regarding management have to be drafted carefully, taking into consideration the age at presentation, rearing sex of the child (in cases of late presentation), psychological evaluation of the child, and acceptability of the family.[10] In our case, the male gender has been assigned after discussion with the parents, and phallic reconstruction procedures have been planned.


We report a case of penile agenesis associated with urethral atresia, malrotated right kidney, and multicystic renal dysplasia of the left kidney. The co-occurrence of aphallia with genitourinary anomalies warrants detailed workup of the renal and urinary tract and addressing the issues of urinary tract drainage and infection with due diligence in order to prevent complications. The assignment of gender and reconstructive procedures poses serious challenges, and decisions have to be undertaken after detailed discussions with parents.

Declaration of patient consent

The authors certify that they have obtained all appropriate patient consent forms. In the form, the legal guardian has given his consent for images and other clinical information to be reported in the journal. The guardian understands that names and initials will not be published and due efforts will be made to conceal identity, but anonymity cannot be guaranteed.

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Conflicts of interest

There are no conflicts of interest.


1Qiang S, Li FY, Zhou Y, Yuan Y, Li Q. Congenital absence of the penis (aphallia): A rare case report. Medicine (Baltimore) 2019;98:e15129.
2Kessler WO, McLaughlin AP 3rd. Agenesis of penis. Embryology and management. Urology 1973;1:226-9.
3Stolar BC, Wiener ES, Hensle TW, Silen ML, Sukarochana K, Sieber WK, et al. Reconstruction of penile agenesis by a posterior sagittal approach. J Pediatr Surg 1987;22:1076-80.
4Gautier T, Salient J, Pena S, Imperto-McGinley J, Peterson RE. Testicular function in 2 cases of penile agenesis. J Urol 1981;126:556-7.
5Choudhury SR, Maji BP. Penile agenesis: An unusual variant. Int Urol Nephrol 1993;25:71-6.
6Haller JR, Schumaker LB, Furness TD. Congenital absence of the penis: Case report. J Urol 1957;78:155-7.
7Bansal RK, Singh J. Congenital absence of penis. Indian Pediatr 1990;27:882-4.
8Joshi A, Gross J, Thomalla JV. Congenital aphallia: Review of pathogenesis and current treatment guidelines. Urology 2015;86:384-7.
9Skoog SJ, Belman AB. Aphallia: Its classification and management. J Urol 1989;141:589-92.
10Chibber PJ, Shah HN, Jain P, Yadav P. Male gender assignment in aphallia: A case report and review of the literature. Int Urol Nephrol 2005;37:317-9.