Not if the resulting HTML is what you would want anyway for SEO purposes. However, you might want to make sure that whatever you use for the "header" includes a way to get any page-specific info into it (such as meta tags keywords/descriptions). I often write them as PHP functions that accept parameters, so the calling page can require_once() the function definitions, then invoke the functions to get the customized output, e.g.:
<?php
require_once $_SERVER['DOCUMENT_ROOT'].'/includes/html_funcs.php';
echo htmlHeader('keyword1, keyword2, keyword3', 'This is a description');
?>
