<div id="header">
<?php
mt_srand((int)date('z'));
$headers=glob(PATH_TO_FILES .'/*.jpg');
$header=mt_rand(0,count($headers)-1 );
?>
<img id="header-image" `src="https://wordpress.stackexchange.com/questions/5232/<?php echo URL_TO_FILES ."https://wordpress.stackexchange.com/".basename($headers[$header]); ?>" alt="header" />
</div>
replace your current header with this. I will of course help you implement this further if you need help. (or if you need the code explained)