My paed and I talked about the difference between Neocate and Nutramigen when my younger son was having problems with milk. (My elder son is allergic to milk -- he's had about 4 or 5 anaphylactic reactions to it.) Here's what he told me: Neocate is built up from amino acids, there's no milk protein in it. Nutramigen is made from hydrolysed milk protein.
Here's a blurb from the Neocate website: www.shsweb.co.uk/neocate/pat/about.htm
Breast milk is the ideal substitute for cow milk in the majority of cases although this may not always be practical. Generally in the past a soy based milk or an extensively hydrolysed protein formula was recommended. A hydrolysed formula contains protein particles small enough to be tolerated by most children. But increasingly, it is recognised that the symptoms of some severely allergic children do not fully resolve on these formulaeresulting in poor growth.
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When they say "breast milk" they mean breast milk from a mother who is not eating any dairy. Milk protein goes into a mother's milk, so the mother cannot eat it if her child is allergic. A milk allergy is a reaction to the milk protein. It is very different than lactose intolerance, which is an inability to digest lactose, a sugar present in all animals (including humans) milk. Nutramigen is a hydrolysed formula, made by chopping up the milk protein into little pieces most (and that's the key, I think) children can handle, ie, the protein bits are small enough to sneak by the out of control immune system. And Neocate doesn't really contain protein -- but it does contain the amino acids with which the proteins are made.
Dunno if that helps. We used Neocate a couple of times, but I gave up milk protein in my diet because I was breastfeeding. He said that it was fine to try either (Nutramigen or Neocate) and simply watch and see if he reacted to Nutramigen. I opted for Neocate, simply because I didn't want to worry about it. If I had continued using formula, I would have probably tried both. Most likely Nutramigen would have been fine. Neocate tastes disgusting, by the way. My elder son used to be allergic to soya, so I didn't try that with the younger (just your average, run of the mill allergy -- hives and swelling). Plus I've got this vague "soya formula is bad" idea. Not prepared to defend that, though.
Anyway, there ya' go. Hope that helps someone.