Index: deprecated.php
===================================================================
--- deprecated.php	(revision 20115)
+++ deprecated.php	(working copy)
@@ -2976,4 +2976,32 @@
 		return $theme;
 
 	return wp_get_theme()->get('Name');
-}
\ No newline at end of file
+}
+
+/**
+ * Accepts matches array from preg_replace_callback in wpautop() or a string.
+ *
+ * Ensures that the contents of a <<pre>>...<</pre>> HTML block are not
+ * converted into paragraphs or line-breaks.
+ *
+ * @since 1.2.0
+ * @deprecated 3.4.0
+ *
+ * @param array|string $matches The array or string
+ * @return string The pre block without paragraph/line-break conversion.
+ */
+function clean_pre($matches) {
+	_deprecated_function( __FUNCTION__, '3.4' );
+	
+	if ( is_array($matches) )
+		$text = $matches[1] . $matches[2] . "</pre>";
+	else
+		$text = $matches;
+
+	$text = str_replace('<br />', '', $text);
+	$text = str_replace('<p>', "\n", $text);
+	$text = str_replace('</p>', '', $text);
+
+	return $text;
+}
+
Index: formatting.php
===================================================================
--- formatting.php	(revision 20115)
+++ formatting.php	(working copy)
@@ -173,30 +173,6 @@
 }
 
 /**
- * Accepts matches array from preg_replace_callback in wpautop() or a string.
- *
- * Ensures that the contents of a <<pre>>...<</pre>> HTML block are not
- * converted into paragraphs or line-breaks.
- *
- * @since 1.2.0
- *
- * @param array|string $matches The array or string
- * @return string The pre block without paragraph/line-break conversion.
- */
-function clean_pre($matches) {
-	if ( is_array($matches) )
-		$text = $matches[1] . $matches[2] . "</pre>";
-	else
-		$text = $matches;
-
-	$text = str_replace('<br />', '', $text);
-	$text = str_replace('<p>', "\n", $text);
-	$text = str_replace('</p>', '', $text);
-
-	return $text;
-}
-
-/**
  * Replaces double line-breaks with paragraph elements.
  *
  * A group of regex replaces used to identify text formatted with newlines and
@@ -207,14 +183,32 @@
  * @since 0.71
  *
  * @param string $pee The text which has to be formatted.
- * @param int|bool $br Optional. If set, this will convert all remaining line-breaks after paragraphing. Default true.
+ * @param bool $br Optional. If set, this will convert all remaining line-breaks after paragraphing. Default true.
  * @return string Text which has been converted into correct paragraph tags.
  */
-function wpautop($pee, $br = 1) {
+function wpautop($pee, $br = true) {
+	$has_pre = false;
 
 	if ( trim($pee) === '' )
 		return '';
+
 	$pee = $pee . "\n"; // just to make things a little easier, pad the end
+
+	if ( strpos($pee, '<pre') !== false ) {
+		$has_pre = true;
+		$pee_parts = explode( '</pre>', $pee );
+
+		$last_pee = array_pop($pee_parts);
+		$pee = '';
+
+		foreach ( $pee_parts as $pee_part ) {
+			$pee .= preg_replace_callback('/<pre(?: [^>]+)*>.+/s', '_autop_newline_preservation_helper', $pee_part) . '</pre>';
+		}
+
+		$pee .= $last_pee;
+		$pee = str_ireplace( '<pre', "\n\n<pre", $pee );
+	}
+	
 	$pee = preg_replace('|<br />\s*<br />|', "\n\n", $pee);
 	// Space things out a little
 	$allblocks = '(?:table|thead|tfoot|caption|col|colgroup|tbody|tr|td|th|div|dl|dd|dt|ul|ol|li|pre|select|option|form|map|area|blockquote|address|math|style|p|h[1-6]|hr|fieldset|legend|section|article|aside|hgroup|header|footer|nav|figure|figcaption|details|menu|summary)';
@@ -239,17 +233,17 @@
 	$pee = str_replace('</blockquote></p>', '</p></blockquote>', $pee);
 	$pee = preg_replace('!<p>\s*(</?' . $allblocks . '[^>]*>)!', "$1", $pee);
 	$pee = preg_replace('!(</?' . $allblocks . '[^>]*>)\s*</p>!', "$1", $pee);
-	if ($br) {
+	if ( $br ) {
 		$pee = preg_replace_callback('/<(script|style).*?<\/\\1>/s', '_autop_newline_preservation_helper', $pee);
 		$pee = preg_replace('|(?<!<br />)\s*\n|', "<br />\n", $pee); // optionally make line breaks
-		$pee = str_replace('<WPPreserveNewline />', "\n", $pee);
 	}
 	$pee = preg_replace('!(</?' . $allblocks . '[^>]*>)\s*<br />!', "$1", $pee);
 	$pee = preg_replace('!<br />(\s*</?(?:p|li|div|dl|dd|dt|th|pre|td|ul|ol)[^>]*>)!', '$1', $pee);
-	if (strpos($pee, '<pre') !== false)
-		$pee = preg_replace_callback('!(<pre[^>]*>)(.*?)</pre>!is', 'clean_pre', $pee );
 	$pee = preg_replace( "|\n</p>$|", '</p>', $pee );
 
+	if ( $br || $has_pre )
+		$pee = str_replace('<autop newline>', "\n", $pee);
+
 	return $pee;
 }
 
@@ -262,7 +256,7 @@
  * @returns string
  */
 function _autop_newline_preservation_helper( $matches ) {
-	return str_replace("\n", "<WPPreserveNewline />", $matches[0]);
+	return str_replace( array("\r\n", "\r", "\n"), '<autop newline>', $matches[0] );
 }
 
 /**