There is no documented or declared limit on the length of the FQL query itself, but there is a limit on the length of the query string (which differs from browsers and web servers, see Compatibility Issues ).
Remember that you do not need to use GET to run the request, and POST will work fine, avoiding the query string limitation.
BTW, if you use the SDK to issue FQL queries, you can manually specify the appropriate HTTP method
Using JS-SDK:
FB.api('/fql', {q:'FQL_QUERY'}, 'post', function(response){
Using PHP-SDK:
$response = $fb->api('/fql', 'post', array('q'=>'FQL_QUERY'));
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