What department are you in? OR In what department are you?

In my opinion they're both grammatical, but the second is not idiomatic.
"In what department do you work?"
I'm not saying you won't hear your second version.

You might also find "What department are you, CIA or FBI?" This would be extremely casual, but you might find it in a movie or on TV.

They both mean the same thing.

Probably a better way to say it is:

Which department are you in?

Welcome to English Forums, Doug; thanks for joining us! [<:o)]

That maple leaf makes me think of how much I miss the New England fall foliage. It's probably all dead by now!

Best wishes, - A.

Thanks for the welcome Avangi. Yes they are mostly on the ground now, but they were beautiful while they lasted. New England is spectacular, I have travelled through there in the Fall.

Thanks for your detailed and clear explanation, Avangi.
DougLewis, thank you too for your reply. You raised the question of when to use "what" and "which" - words that are for the most part interchangeable, but not always. The kind of words non-natives love.

Kunsan

• In what department are you?

This one sounds about as good as Wiliam Hung singing "she bangs"

From the perspective of conversational english I would say that a person saying these sentences would mean;

- What club are you in?... meaning what kind of club are you in.

- Which club are you in?... meaning of several clubs, which one are you in.

DL.

Thanks, DL, I appreciate your comment very much. I think I get the nuance. Yet would it be correct to conclude that in an ordinary conversation both questions can be used more or less interchangeably?
For example, I want to know in what (which?) club you are. Which question do I ask?

Hi,

Could you tell me if there is a difference between the following two sentences?

Yes. #1 sounds natural. #2 sounds formal, fussy, even perhaps pedantic.

What department are you in?

• In what department are you?

Clive

Again in a conversational context, for me the questions posed, without further context would seem to elicit this kind of conversation...

A) What club are you in? (Tennis? soccer? crib? or? and so forth)

After the type of club is established then...

B) Which (tennis) club are you in?

I expect there will be differences of opinion and in conversation there