Jodi,
Acne is a known side-effect of prednisone. Not all patients are affected in this way but it's one more reason why you'll be glad when your son can get off prednisone. However, the priority has to be on helping your son's recovery from SAA (I'm glad to hear it's going well!) so he may have to cope with insomnia and acne for now in order to make sure his blood counts stay stable. But let his doctor know of your concern and ask if there's a risk of scarring or if any dosage changes are called for.
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