Nagato

is the recognized leader of Akatsuki and is from Amegakure. He is referred to as "leader" by all Akatsuki members except for Konan, who refers to him by his name. Although he directs the actions of the other members and maintains authority over them, Pain takes orders from Tobi, who is actually Madara Uchiha. In addition to acting as Akatsuki's leader, Pain was the leader of the winning faction in the Land of Rain's latest civil war.

Trivia

 * Each body of the "Six Paths of Pain" has a designation matching each of the Six Paths of reincarnation in Buddhism: Deva, Asura, Human, Animal, Preta, and Naraka. It is possible that Kishimoto intentionally derived the designations from Buddhism, however, no connections have been officially confirmed.
 * Each body has 6-7 piercings which is a pattern Kishimoto plays on. (Pain usually has 6 bodies on hand)

Speculations
Before chapter 363 when the face of Pain has actually been fully shown, there was a theory highly popular in fandom that stated the Akatsuki Leader is the Fourth Hokage. This speculation has been recently resolved as incorrect, however even in the light, Pain's Yahiko body resembles Minato Namikaze in ways. Some fans still believe Pain is the Fourth Hokage in disguise as not to have people know who he is since Pain has multiple bodies, but this fact has yet to be proven or disproved. Another speculation is that the multiple bodies of Pain are a variant of his Shapeshifting Technique, used to split his chakra and abilities into multiple bodies.

It can also be inferred that Pain has a seventh body, because in the message Jiraiya left, it mentions that "the real one is not with them". This could mean that the head body, which could be Nagato, controls his six bodies from a distance, and as long as the seventh one survives, Pain can't die.

It has also been speculated in the past that Pain could be the Sage of the Six Paths. However, this theory died out long ago.

If you look closely at the piercings of the Pain bodies faces you can see: first body has seven piercings in both ears and six piercings in his nose (if you think it over there are only three piercing in the nose), second body has seven circle piercings on his face, third has body six circle piercings on his face, fourth body has six piercings under his lips, fifth has body six piercings on top of his head, sixth body has seven circle piercings on his face, seventh body has seven piercings on her face. This seems to be connected with the six/seven theme with Pain. Whether it is a clue to how the bodies work or not is unknown.

The piercings in Pain's bodies also appear to correspond with the abilities of each body. For example, Pain's fifth body has five spikes protruding from his head, while it is seen in the manga that his head opens up as part of a technique. Pain's first body also has piercings near the mouth and ears. The person controlling Pain may have pierced the body there so he could communicate through the Deva path.

Quotes

 * "We're both of the same breed, after all...Motives for war are not of concern. Religion, ideology, resources, land, spite, love, or just because...no matter how pathetic the reason, it's enough to start war."
 * "Sensei...you're still just a normal person. But I, living in an infinite universe of pain, have grown from a person into something more."
 * "People who have a weapon will inevitably use it... Hundreds of millions of people will be killed instantly. And the survivors would be completely terrified! All the people...all the world...Will learn what true pain is!!"
 * "It's time... for you to witness "The Six Paths of Pain".
 * "This is nothing compared to the Pain the world will suffer."
 * "Now thats your opinion...Sensei."