Even though the attack comes a day after the indictment of several prominent Anonymous and LulzSec members, the attack wasn't a protest against the happenings.
"Anonymous decided today to besiege your site in response to the doctrine, to the liturgies, to the absurd and anachronistic concepts that your for-profit organisation spreads around the world," explained the group on its website.
They accused the Vatican of a great number of things beginning with the murder of its critics throughout the centuries, child molesting by its priests, the banning of condom use and abortion, and influencing heavily and negatively the everyday lives of the Italians.
"This attack is not against the Christian religion or the faithful around the world but against the corrupt Roman Apostolic Church," they concluded.
The websites hit are available again.
This is not the first time Anonymous targeted the Vatican's online assets. According to a report recently released by Imperva, they tried to first compromise and then DDoS several of its websites in 2011, but were unsuccessful.