Ask the Nutritionist: Dr. Getty's Forum for Equine Nutrition
Welcome to my forum.
Here you will find more than 6 years of questions and my answers. It is searchable and offers a great deal of information.
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All the best,
Dr. Getty
Hi Susan,
Feeding flaxseeds whole is not especially harmful if fed in small quantities, but it is a waste since your horse is not able to break open the small seeds to get at the inside pulp. The seeds will simply pass through his digestive system undigested. The bacterial flora in the hind gut may ferment some of the fibrous hull, but your goal in feeding flaxseeds it to provide nutritious omega 3 fatty acids. And, your horse is not getting these the way you're currently feeding.
So, there are a couple of options. The first is to grind them in a coffee grinder and feed 1/4 cup each day. You'll need to grind no more than 3 or 4 days worth and keep the meal refrigerated, since it can go rancid very easily.
But another problem with this method is that the calcium/phosphorus ratio in flaxseeds in inverted, so unless you are feeding a feed that is high in calcium, you may be providing too much phosphorus by feeding them ground.
The second option is to purchase a stabilized flaxseed meal product that does not require refrigeration, and is more economical. Nutra Flax is a pure flaxseed meal product that has added calcium to provide more calcium than phosphorus. And Nutra Flax does not have added grain, like other flaxseed meal products on the market.
So, I hope this is helpful. Please let me know if you have any more questions.
All the best,
Dr. Getty 
Where are you from? Bayfield, CO