Purpose We determined whether 5 alpha-reductase type 2 mutations are present in boys with isolated hypospadias. Materials and Methods Penile skin tissues obtained at surgery during hypospadias repair were examined for 5 alpha-reductase type 2 mutations by single strand conformational polymorphism and deoxyribonucleic acid sequence analysis. Clinical data, including family history of hypospadias and preoperative position of the urethral meatus, were correlated with the genetic findings. Results Of the 81 specimens examined 7 (8.6%) involved a mutation in at least 1, 5 alpha-reductase type 2 gene, while 2 patients had mutations in both alleles. The mutations identified were A49T, L113V and H231R. The A49T mutation in 5 patients was the most common (71%) and it was generally present in less severe forms of hypospadias. To our knowledge neither the A49T nor the L113V mutation has been previously reported in association with 5 alpha-reductase type 2 deficiency and to date they have only been identified in cases of isolated hypospadias. Family history was negative in the 7 patients with 5 alpha-reductase type 2 mutations but positive in 5 without mutations. Conclusions Some boys with isolated hypospadias have a mutation in at least 1 gene for 5 alpha-reductase type 2. This finding suggests that a partial deficiency of 5 alpha-reductase activity and inadequate levels of dihydrotestosterone in the fetal urethra may be sufficient to cause the phenotype of hypospadias without other clinical features of 5 alpha-reductase deficiency. Family history may not be reliable for determining which boys with hypospadias are likely to have such mutations.