Before the game's release, Naughty Dog's co-president Christophe Balestra posted a picture of the company's network drive on Twitter.

The picture showed that Uncharted 3's assets filled a 25 terabyte (25,600 gigabytes) hard drive.

Right before you start climbing the ruins in the beginning of Chapter 8 you can see a sign on the gate that ironically says "Climbing Forbidden on Ruins".

After the big bar fight in the beginning of the game, if you walk over to the other side of the bar instead of following Sully, you can find a newspaper that reads, "Scientists are still struggling to understand deadly fungus." This is referencing the fungal infection in the game "The Last of Us." This easter egg was planned to be removed by the development team before the game was shipped (as they were not planning to reveal the game until much later) but forgot about it and released the game with the easter egg still in.

The dry docks and cruise ship chapters run an ocean simulation. The movement of the cruise ship in those chapters is not an animation on loop, but generated by its interaction with the ocean.

There are several easters eggs amongst the plaques and graffiti in The Pelican Inn can be found;

• On the scoreboard for the darts game, a plaque with a lion emblem and a calendar have the names Reuban Shah and Brian Beppu on them. Reuban is an Environment Modeler and Brian is a Texture Artist, both for Naughty Dog.
• A larger plaque has not only Reuban Shah and Brian Beppu, but also Charlotte Francis, what is thought to be "Anthony Vaccaro" who is also an Environment Modeler, Paul Moya, David Witters and two more that, at the moment, can't be properly read due to graphical limitations. These aforementioned are all also Naughty Dog employees.
• The bathroom also has a small name drop, with graffiti saying "Charlie Horsey", which is a bit of a moniker Brian Beppu used in the past.
• "ND1" and "ND1 DOG", can be found as a beer and also a sticker in the pub's restroom, which likely means Naughty Dog. The Naughty Dog paw-print logo is also found in the restroom.
• Finally, a series of plaques with the Uncharted series titles (Uncharted, Uncharted 2 and Uncharted 3), with their respective release dates on them (2007, 2009 and 2011.)

Before Uncharted 3: Drake's Deception was released, Charlie Cutter was introduced as an antagonist who was working for Katherine Marlowe. In the E3 2011 trailer, scenes of him playing the role of the villain were shown. But when the game was ultimately released, it was revealed that he was in fact on Nathan Drake's side.

During a cutscene at the end of chapter 9, you can see Sackboy from the LittleBigPlanet series, hanging on the front mirror of the bus.