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The prejudice that you may find against DOs is not present throughout all MD residencies as you suggested. Its confined to the more competitive specialties (ortho, derm, rad, etc). If you are dead set on going to an MD residency in one of those specialites, then its something you should think about, but there are DO residencies as well.
Also neuro, ENT, cardiology, etc. DO schools are aggressively expanding class sizes and new ones are opening all over the place (including for-profit schools). Meanwhile, the number of spots open for many residencies is staying fairly steady. This could mean higher difficulty for a DO hoping to match into even a moderately competitive residency.