This case report describes a three-year-old Friesian stallion with hypospadias. Physical examination revealed a ventrocaudal deviation of the shaft of the penis and an incomplete glans penis. The urethral opening was 4 cm in length, slit-like and had a mucous membrane covering. A short fold ran from the ventral aspect of the anus and ended with a non-pigmented hairless area of skin. A human choriongonadotropin (hCG)-stimulation test resulted in an increase in the plasma levels of estrogen sulfate and testosterone, indistinguishable from that of a normal stallion. The karyogram had a normal number of chromosomes at 2n=64. The stallion was castrated, and histological evaluation of the testicular tissue was unremarkable. In contrast to other animal species and human beings, hypospadias is a rare congenital abnormality in stallions, the cause of which could not be elucidated in our patient.