The testicular function of men previously operated for hypospadias has been sparsely investigated. Therefore, we investigated semen quality and reproductive hormones of 92 men with isolated hypospadias (IH) and 20 with hypospadias and additional genital disorders (HAGD) and compared with similar results from young men from the general Danish population. All participants lived the Copenhagen area of Denmark. Additionally, fertility information on 1083 men registered as operated for hypospadias was retrieved from national registries. The semen quality of men with IH did not differ from controls, but was reduced in men with HAGD. Median values for IH and HAGD were, respectively: sperm concentration 52 and 32 million (mill)/mL (p = 0.02), total sperm counts 173 and 101 mill (p = 0.03), motile spermatozoa 70 and 58% (p = 0.007) and morphological normal spermatozoa 9 and 4% (p = 0.004). Men with IH had a slight increase in follicle stimulating hormone and luteinizing hormone levels, whereas men with HAGD had more pronounced disturbances. 24.0% of the 1083 men operated for hypospadias were registered as fathers to at least one child, whereas the corresponding number in the general age-matched population was 29.4% (p < 0.01). In conclusion, the majority of men with IH had normal semen quality, whereas it was reduced for men with HAGD. However, reproductive hormone levels indicated a subtle impairment of testicular function also in men with IH. An observed lower number of fathers among men with hypospadias may be because of psychosocial aspects, sexual dysfunction or reduced semen quality or a combination of these factors. Our results should be reassuring for patients with mild forms of IH and their relatives. They can be informed that hypospadias in such cases is not generally associated with poor semen quality. Particularly among patients with HAGD, several may, however, need fertility treatment to reproduce.