$re = '/(?s).*?(<div id="start">.*?<div id="end">)(?:(?:(?!<div id="start">).)*$)?/m';
$str = 'Stuff I dont need before
<div id="start">
blablabla11
blablabla12
<div id="end">
Stuff I dont need in the middle
<div id="start">
blablabla21
blablabla22
<div id="end">
Stuff I dont need in the middle2
<div id="start">
blablabla31
blablabla32
<div id="end">
Stuff I dont need in the end';
$subst = "$1\n\n";
$result = preg_replace($re, $subst, $str);
echo "The result of the substitution is ".$result;
Please keep in mind that these code samples are automatically generated and are not guaranteed to work. If you find any syntax errors, feel free to submit a bug report. For a full regex reference for PHP, please visit: http://php.net/manual/en/ref.pcre.php