Like ALL said, you need to echo each individual statement. You als need to ensure that the Javascript code is inside script tags.
PHP Code:?>
<script type="text/javascript">
<!--
var myarray = Array(<?php echo(count($myarray)) ?>);
<?php for($x = 0; $x < count($myarray); $x++): ?>
myarray[<?php echo($x) ?>] = <?php echo(htmlspecialchars($myarray[$x])) ?>;
<?php endfor; ?>
//-->
</script>
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