They both mean the same thing. " is more common in British English, perhaps, but as far as I know, both are used in all varieties of English. "have got" is probably the only case in English where the present perfect form is used with present meaning.
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Do you have a headache? (Now, this time, not habitutal.)
Are you having one of your headaches? (Now, this time, not habitual.)
Is it so?