Hypospadias,characterized by abnormal position of the urethral opening,is the second most common congenital anomaly in men.Its incidence is increasing year by year,and it has become the fourth largest birth de-fect disease in China.Not only does it bring both physical and psychological distress to the patients,but its surgical repair and long-term postoperative management also occupy a large amount of social economic and medical re-sources.Hypospadias can be isolated or present as a manifestation of some syndrome.At present,there are a varie-ty of methods used to define and evaluate hypospadias,and it is imperative to develop a uniform classification standard to standardize care and surgical methods.In humans,the normal development of the penis structure has experienced an early androgen-independent stage and a late androgen-dependent sexual differentiation stage.In ad-dition to genetic changes,endocrine or external environmental influences can cause damage or loss of the basic ele-ments of penile development,which can induce hypospadias.Therefore,the disease is the result of genetic,endo-crine and environmental factors and their interaction,with genetic factors generally considered to be more important than others.Based on different population cohorts,this paper elucidates the causes of hypospadias from the per-spective of classical genetic variation,involving gene polymorphism,single nucleotide polymorphism and copy num-ber variation of genes in normal biological processes such as growth differentiation of reproductive nodules,gonadal development and testis differentiation,androgen and estrogen production,etc.Moreover,the candidate genes relat-ed to human hypospadias are summarized.This paper will provide theoretical basis for the screening,intervention and clinical treatment of hypospadias,and contribute to improve the quality of birth population.