You can do it like this:
$facebook = new Facebook(array(
'appId' => FB_ID,
'secret' => FB_APP_SECRET,
'cookie' => true,
));
$fql = "SELECT id FROM profile WHERE id IN (SELECT uid2 FROM friend WHERE uid1=me())";
$response = $facebook->api(array(
'method' => 'fql.query',
'query' =>$fql,
));
This will return the id of the mutual friends. Hope this helps you :)
EDIT:
If you want to get the mutual friends between you and id=13245 then you can do like:
$facebook = new Facebook(array(
'appId' => FB_ID,
'secret' => FB_APP_SECRET,
'cookie' => true,
));
$fql = "SELECT uid1, uid2 FROM friend WHERE uid1 IN (SELECT uid2 FROM friend WHERE uid1=me() AND uid2 = '13245' ) AND uid2 IN (SELECT uid2 FROM friend WHERE uid1=me())";
$response = $facebook->api(array(
'method' => 'fql.query',
'query' =>$fql,
));
It will return all mutual friends id.
Hope this gives you what you want.