Give (or have your vet give) your stallion only one or two injections per day; wait at least a week before giving any more.

http://equisearch.com/horses_care/health/breeding/eqmyth642/index2.html


....10. You shouldn't vaccinate your stallion during breeding season--the vaccine may adversely affect sperm. Busted! Although old-time vaccines used to make a horse sick and feverish for a day or 2 (which we already know can adversely affect sperm), equine vaccines available today generally don't cause these problems.
However, stress definitely has a negative effect on all bodily functions, including reproductive processes-and giving your stallion multiple vaccines on the same day could be stressful for him. And, even when the injection is given properly, once in a while the injection site will get swollen, hot, sore, and stiff for a day or 2 afterward. The resultant discomfort can interfere with your stallion's libido, as well as his ability to tease, mount, and ejaculate.
To reduce the risk of vaccination-related stress, follow these tips:
Choose your stallion's vaccines wisely, in conjunction with your vet's advice. That is, don't just vaccinate your stallion willy-nilly for every disease ever discovered.
Acquire vaccines from a reputable source, so you know they've been properly stored. If stored improperly, they can become spoiled or contaminated, or otherwise rendered ineffective.
If possible, have your vet give all injections to ensure they're done properly and given in the right location.
Use (or have your vet use) only preloaded, single-dose syringes, rather than vaccine drawn from a multiple-dose vial, as they're less likely to be contaminated.





Give (or have your vet give) your stallion only one or two injections per day; wait at least a week before giving any more.