Aim: Penile agenesis, defined as aphallia, is an extremely rare congenital anomaly. Though this condition is diagnosed clinically, it may be associated with various ano-rectal and systemic malformations. Until date, very few cases of aphallia have been reported globally. The most important dilemma in such cases lies in the treatment associated with gender reassignment. Case Report: We report a rare of case aphallia as a solitary presentation, in a neonate born in a rural hospital of West Bengal and the dilemma imposed on the parents regarding the management. Discussion and Conclusion: The confusion regarding the surgical intervention associated with the psyco-sexual influence is a major hindrance.