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On occasion, my cat will sit there with their mouth open, usually after smelling something new.

It looks similar to panting, but without the heavy breathing or a protruding tongue.

What is the reason for this? Is it a reaction to particular smells? We refer to it as the "stink face", but does it really indicate that a scent was disagreeable?

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This would be the Flehmen response: http://en.wikipedia.org/wiki/Flehmen_response

Many animals will do this to move air over a specialized scent gland which is used to identify pheromones for reproductive and communication purposes. Our cats will do it for anything they think smells interesting, usually before they go to investigate more closely.

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    I think "organ" would be better than "gland", it is called vemoronasal organ. (the deleted answer made it show up in the first page, I didn't intend to dig it up just for that...) – Cedric H. May 6 '15 at 15:51

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