Cigar was a famous racehorse who commanded a huge stud fee - and then failed to get a single mare in foal. All kinds of infertility treatments were tried, including putting him out to pasture and just leaving there in the hope it was just stress. After nothing worked, he spent the rest of his life at the Kentucky Horse Park.
Cigar's problem was low sperm quality, but stallions can also be rendered sterile by low sperm count. Cryptorchid stallions tend to have low sperm quality in the descended testicle and as we now know that the condition itself is genetic, cryporchids are routinely gelded.
Two other conditions common in stallions are contamination of the semen with blood or urine. The former tends to be temporary, caused by an infection. The latter is a bladder deformity and cannot always be treated.
Other issues that can cause infertility in stallions are breeding fatigue (breeding too many mares, resulting in a loss of libido), back or hind limb injuries that can make it hard for them to mount the mare, fever.
Another cause is that some stallions can produce enough sperm in the off season to actually block their tubes. They keep producing sperm and not ejaculating it. Collecting sperm in the off season or oxytocin treatments often resolve it.
And, of course, genetic conditions can also affect male fertility - sex reversal syndrome, for example.
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