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The choice to substitute formulations has much to do with its intended purpose, severity and economic factors.  However, when it comes to autism, substitution must also consider individual biology.  
Here is what Wiki Answers has to say:
“It is also important to note that the amount of drug which makes it into the bloodstream (bioavailability) can vary significantly for generic drugs; the bioavailability of generics is required to be within 20% of the branded drug, meaning it can be 20% lower to 20% higher. This can make a significant difference for drugs which are very dose-dependent. Also the amount of active ingredient in the generic only needs to be within 7% of the branded drug. All in all the generic might end up quite a bit less or more potent than the branded drug.”
“Two drugs are considered pharmaceutical equivalents when they contain the same chemically active ingredient(s) and are identical in dosage form and strength. Tetracyclines such as minocycline are complex with many properties that may play an important part in treatment response in the arthritic patient. The fact that patients in remission (sometimes for years) while on antibiotic therapy saw a gradual return of symptoms when switched to a generic alerted us to a potential problem with some generics. In three test patients, these symptoms began to reverse immediately upon a return to the brand name version of the drug.

Pharmaceutical equivalence may be affected by many things.

  1. variations in inert ingredients
  2. plants in different parts of the world may produce ingredients that vary in quality, by batch and manufacturing methods. Until recently (this article was published in September 18, 2008), 80% of drug ingredients came from plants in Western Europe. According to a NY Times article April 11, 1996, that is changing. Many ingredients are now being used from plants in China, Japan, South Korea, India and Eastern Europe where they are produced more cheaply. Bob Milanese, president of the National Association of Pharmaceutical Manufacturers, indicates that only a handful of these plants meet FDA standards. “Some others are questionable” due to the difficulty in finding people and budget to “get over and inspect these plants.” Another factor which affects generic quality cited by the same article is the international buy outs and diversification allowing the combination of questionable ingredients into generic production.
  3. In oral drugs, capsule content may be 7% over or 7% under the stated content, e.g. a 100 mg. capsule may be as low as 93 mg. or as high as 107 mg.

Given all this, the difficult task of determining the appropriate dosage of a specific drug for a specific patient seems to an impossible task, destined to fail.  This does not make sense for anyone involved… including the insurance companies who will have to foot the bill for emergency services and therapy that might have been avoided had the proper meds been used.  I acknowledge the need to contain medical costs.  But the savings achieved by substituting generics, frequently can not justify the increase in unnecessary human suffering.

There is a great deal of information (both good and bad) on the Internet.  My recommendation is to have an open discussion with your doctor about your options.