Index: wp-login.php
===================================================================
--- wp-login.php	(revision 6342)
+++ wp-login.php	(working copy)
@@ -1,4 +1,5 @@
 <?php
+require( dirname(__FILE__) . '/wp-includes/class-phpass.php');
 require( dirname(__FILE__) . '/wp-config.php' );
 
 $action = $_REQUEST['action'];
@@ -184,7 +185,10 @@
 
 	// Generate something random for a password... md5'ing current time with a rand salt
 	$new_pass = substr( md5( uniqid( microtime() ) ), 0, 7);
-	$wpdb->query("UPDATE $wpdb->users SET user_pass = MD5('$new_pass'), user_activation_key = '' WHERE user_login = '$user->user_login'");
+	// By default, use the portable hash from phpass
+	$hasher = new PasswordHash(8, TRUE);
+	$new_hash = $hasher->HashPassword($new_pass); 
+	$wpdb->query("UPDATE $wpdb->users SET user_pass = '$new_hash', user_activation_key = '' WHERE user_login = '$user->user_login'");
 	wp_cache_delete($user->ID, 'users');
 	wp_cache_delete($user->user_login, 'userlogins');
 	$message  = sprintf(__('Username: %s'), $user->user_login) . "\r\n";
Index: wp-includes/pluggable.php
===================================================================
--- wp-includes/pluggable.php	(revision 6342)
+++ wp-includes/pluggable.php	(working copy)
@@ -1,5 +1,7 @@
 <?php
 
+include_once(ABSPATH . WPINC . '/class-phpass.php');
+
 	/* These functions can be replaced via plugins.  They are loaded after
 	 plugins are loaded. */
 
@@ -298,6 +300,23 @@
 	} else {
 		// If the password is already_md5, it has been double hashed.
 		// Otherwise, it is plain text.
+		if(strlen($login->user_pass) > 32 && !$already_md5) {
+			//If the stored hash is longer than an MD5, presume the
+			//new style phpass portable hash.
+			$hasher = new PasswordHash(8, TRUE);
+			if ($hasher->CheckPassword($password, $login->user_pass)){
+				//Successful match
+				return true;
+			} else {
+				//Fail!
+				$pwd = '';
+				return false;
+			}
+		} elseif (strlen($login->user_pass) > 32 && $already_md5) {
+			//If password has already already_md5 it has been double hashed
+			$test = md5($login->user_pass);
+			return ($test == $password);
+		}
 		if ( ($already_md5 && md5($login->user_pass) == $password) || ($login->user_login == $username && $login->user_pass == md5($password)) ) {
 			return true;
 		} else {
@@ -456,8 +475,10 @@
 
 if ( !function_exists('wp_setcookie') ) :
 function wp_setcookie($username, $password, $already_md5 = false, $home = '', $siteurl = '', $remember = false) {
-	if ( !$already_md5 )
-		$password = md5( md5($password) ); // Double hash the password in the cookie.
+	$user = get_userdatabylogin($username);
+	if ( !$already_md5) {
+		$password = md5($user->user_pass); // Double hash the password in the cookie.
+	}
 
 	if ( empty($home) )
 		$cookiepath = COOKIEPATH;
Index: wp-includes/registration.php
===================================================================
--- wp-includes/registration.php	(revision 6342)
+++ wp-includes/registration.php	(working copy)
@@ -1,5 +1,7 @@
 <?php
 
+include_once(ABSPATH . WPINC . '/class-phpass.php');
+
 /**
  * Checks whether the given username exists.
  * @param string $username Username.
@@ -52,8 +54,10 @@
 		$update = true;
 	} else {
 		$update = false;
-		// Password is not hashed when creating new user.
-		$user_pass = md5($user_pass);
+		//If this is a new user being created, we need to
+		//use the phpass portable hash
+		$hasher = new PasswordHash(8, TRUE);
+		$user_pass = $hasher->HashPassword($user_pass);
 	}
 
 	$user_login = sanitize_user($user_login, true);
@@ -154,7 +158,9 @@
 	// If password is changing, hash it now.
 	if ( ! empty($userdata['user_pass']) ) {
 		$plaintext_pass = $userdata['user_pass'];
-		$userdata['user_pass'] = md5($userdata['user_pass']);
+		//Use the new phpass portable hash
+		$hasher = new PasswordHash(8, TRUE);
+                $userdata['user_pass'] = $hasher->HashPassword($userdata['user_pass']);
 	}
 
 	// Merge old and new fields with new fields overwriting old ones.
@@ -205,4 +211,4 @@
 	return wp_create_user($username, $password, $email);
 }
 
-?>
\ No newline at end of file
+?>
Index: wp-includes/user.php
===================================================================
--- wp-includes/user.php	(revision 6342)
+++ wp-includes/user.php	(working copy)
@@ -1,5 +1,7 @@
 <?php
 
+include_once(ABSPATH . WPINC . '/class-phpass.php');
+
 function get_profile($field, $user = false) {
 	global $wpdb;
 	if ( !$user )
@@ -16,8 +18,14 @@
 // TODO: xmlrpc only.  Maybe move to xmlrpc.php.
 function user_pass_ok($user_login,$user_pass) {
 	$userdata = get_userdatabylogin($user_login);
-
-	return (md5($user_pass) == $userdata->user_pass);
+	if (strlen($userdata->user_pass) > 32) {
+		//The hash is longer than MD5, so presume the new phpass portable hash
+		//is being used.
+		$hasher = new PasswordHash(8, TRUE);
+		return($hasher->CheckPassword($user_pass, $userdata->user_pass));
+	} else {
+		return (md5($user_pass) == $userdata->user_pass);
+	}
 }
 
 //