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I can understand saying "I was wondering how is A doing?" is not grammatically correct. Instead we should say "I was wondering how A is doing?".

On the other hand, I was wondering which one or both is grammatically correct:

  1. "I was wondering what are the differences between A and B?"
  2. "I was wondering what the differences between A and B are?"

In my opinion both are correct, and the first one seems more balanced the the second, as A and B can be long.

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2 Answers 2

The problem with "I was wondering what are the differences between A and B" is that the segment "I was wondering" is a complete sentence and "What are the differences between A and B?" is a complete sentence. It sounds funny smushing them together without punctuation:

I was wondering: What are the differences between A and B?

I was wondering, what are the differences between A and B?

The problem disappears with "I was wondering what the differences between A and B are" because "What the differences between A and B are" is not a sentence and the whole sentence is more like the form "I was wondering what these are."

Restructuring a sentence because a bit in the middle is getting too long is okay to do but there are other ways to deal with the same problem:

I was wondering about A and B. What are the differences here?

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Actually, I would prefer this variant:

I was wondering what the differences are between A and B.

Your #1 is incorrect. #2 is permissible, but as mentioned it may be difficult to parse when A and B is very long.

Note that all of these sentences should be punctuated with a period, not a question mark.

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+1 for the variant. Much better than my variant. :) –  MrHen Apr 13 '11 at 20:02

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