Rationale: Absence of the penis, known as aphallia, is a very rare congenital anomaly. It is believed to be a result of either the absence of the genital tubercle or its failure to fully develop and is associated with the level of hormones and chromosomal rearrangements. The failure of the genital tubercle influences the development of the penis and partly depends upon testosterone secreted by Leydig cells of the testis. Chromosomal polymorphisms may affect the functions of protection and regulation, potentially leading to susceptibility to congenital diseases. Herein, an extremely rare case of a congenital absence of the penis is described. Patient concerns: A 3-month-old was brought to the OPD by his parents with complaints of absence of penis since birth and urine being passed rectally. When he was born, he was registered as a boy because his chromosomes were 46XY but with 9qh+. Local examination revealed the total absence of the penis. The scrotum was well developed. The testes were palpable bilaterally. The anal opening was located normally. No urethral orifice could be identified. However, his parents had not yet decided whether to accept treatment. The child has been lost to follow up. Diagnosis: Congenital absence of the penis (aphallia) (46 XY normal male karyotype). Interventions: We explained the nature of the abnormality and management options to the parents. However, it was much regretted that the patient was too young to make a decision and that his parents had not made a decision yet. They left without any further contact. Outcome: Because the parents left our hospital without any contact, it has not been possible to develop a follow-up plan. Lessons: In consideration of the rarity and devastating psychosocial consequences of this case, we accordingly call for active cooperation with doctors to minimize the negative impact of this malformation. Early assignment of gender avoids confusion and contradiction. Parental confidence solidifies the child's own confidence in his or her gender.

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