Fedora Linux uses pam module called pam_succeed_if.so for its authentication.Default configuration of this module blocks root login using GUI.
STEP 1: Login as a Normal User.
STEP 2: Open the terminal and use your favourite text editor like vim or gedit to open the
/etc/pam.d/gdm.
# su -c “vim /etc/pam.d/gdm”
STEP 3: Comment the following line ‘auth required pam_succeed_if.so user !=root quiet’
# auth required pam_succeed_if.so user != root quiet
STEP 4: Also open /etc/pam.d/gdm-password and put comment in front of the below line:
# auth required pam_succeed_if.so user != root quiet