I can't seen to figure this problem out after consulting the faq on the issue and Google. I have written a custom CMS and trying to touch up the Mod Rewrite work done. The site in the main directory works fine with my rules, however, I found the need to install a directory with the CMS to test out another site and it doesn't work that well... I have the rules set up so that when you visit localhost/category you are 301 redirected to localhost/category/ , just appending the / at the end simulating a directory. In the directory, when I try to access this the redirect directs from localhost/webmasters/category to localhost/category/. Here is my htaccess rules... Options +FollowSymlinks RewriteEngine On RewriteBase /webmasters/ # Write categories that do not end with a trailing slash # to end with a trailing slash ( 301 redirect ) RewriteCond %{REQUEST_FILENAME} !-f RewriteCond %{REQUEST_URI} !(.*)/$ RewriteCond %{REQUEST_URI} !.html$ RewriteRule ^(.*)$ /$1/ [L,R=301] # Core rewrites # Handles the primary rewrite, CMS handles the rest :D RewriteCond %{REQUEST_FILENAME} -f RewriteRule ^(.*) $1 [L] RewriteCond %{REQUEST_URI} !-d RewriteCond %{REQUEST_FILENAME} !-d RewriteRule ^(.*)$ index.php?category=$1/ [L] RewriteRule ^([a-z_]+)/([^/]+/)$ index.php?category=$1 Code (markup): This might get even more confusing in the fact that only one rewrite is needed, its only on the first index.php?Category=whatever. I've exploded the URL into parts starting from $_GET['category'] ( if you don't know PHP, sorry ), so the anything following /category/ I can get without the need for mod rewrite. This solution ended up much more simply in the end, aside from writing the htaccess ( which I don't have a problem with other than being in sub directory ). Any help on this? Been confusing me for so long now...