flax seed

Grind them - otherwise they just pass right through same as they went in. I use a coffee grinder or my little blender thing (it's not the bullet but similar - I forget what I have).

What she said. Grind them. I have a Bullet, which grinds them up nicely, but a blender may do the trick as well. Just put in on the grind setting. Another suggestion is to just grind up enough to use for a week or so at at time and put it in a sealed container or ziploock in the fridge. They lose their potency more quickly after they are ground up.

NO! Don't grind them! They are tasty, amazing little things. I love them whole on my oatmeal, in my cereal, and on my salad, yum! Yes, they do tend to come out the other end whole, but you will crush lots of them. The dark flaxseed is the tastiest. Remember that the nutrients in flax seed are effected by heat, so do not add them to anything while you are cooking it, wait until after it is cooked and sprinkle on before serving, so that you do not damage the omega-3's.
My 6 year old daughter eats them by the handful just like nuts.
If you do grind them store them in the freezer to keep the nutrients from disappearing. I keep mine whole in the freezer and just pull out a small container every week to put in the fridge for daily use.
Note: ground flaxseed and boiling water can be used in place of eggs in baking.