Year-by-year, there has been an increasing number of literature on hypospadias, and most of them are mainly focused on two aspects, namely surgical techniques and aetiology, including the molecular mechanism and associated environmental factors. Surgical techniques and nursing levels are being continuously improved. However, in stark contrast, the study of aetiology still lags behind. Up to now, there is still no consensus on the aetiology of hypospadias, including the molecular mechanism and associated environmental factors. To obtain an overall and latest result on the aetiology, we reviewed published literature regarding the aetiology of hypospadias including the molecular mechanism and associated environmental factors in PubMed in the last 5 years. Thirty-seven studies on the aetiology of hypospadias including molecular mechanism and associated environmental factors were found, of which 25 were about associated environmental factors, and they were described according to the aspects of chemicals, parental characteristics, nutrition and hormones. The remaining studies were about the hormone-dependent phase of molecular mechanism, namely androgen-related genes and oestrogen-related genes. Furthermore, the various points of view were classified and discussed in detail.