I did some alterations as I wanted to backup more than just the home dir. The include file determines what is to be backed up now. The new rsync command (now uses in and excludes and "/" as src) : $RSYNC \ -va --delete --delete-excluded \ --exclude-from="$EXCLUDES" \ --include-from="$INCLUDES" \ / $SNAPSHOT_RW/home/daily.0 ; Exclude file (the stuff we dont want) : #rsync script exclude file **/.pan/messages/cache/ **/.phoenix/default/*/Cache/ **/.thumbnails/ **/Desktop/Trash/ Include (what dirs to be included): #rsync script include file /home/ /home/** /var/ /var/www/ /var/www/** /etc/ /etc/** - * Note the "- *" for excluding everything except the dirs mentioned in the include file. Also note the "/var/" entry. To backup /var/www/* , you need to include /var/